Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Switch from ETLHelper to DataIntegrationHelper #154

Merged
merged 1 commit into from
Apr 9, 2024
Merged

Switch from ETLHelper to DataIntegrationHelper #154

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 3 additions & 11 deletions PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,38 +17,30 @@
package org.labkey.test.tests.pmr;

import au.com.bytecode.opencsv.CSVReader;
import org.apache.hc.client5.http.classic.methods.HttpUriRequest;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.remoteapi.Command;
import org.labkey.remoteapi.CommandResponse;
import org.labkey.remoteapi.PostCommand;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.remoteapi.query.TruncateTableCommand;
import org.labkey.serverapi.reader.Readers;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
import org.labkey.test.Locators;
import org.labkey.test.ModulePropertyValue;
import org.labkey.test.TestFileUtils;
import org.labkey.test.TestTimeoutException;
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.External;
import org.labkey.test.categories.LabModule;
import org.labkey.test.tests.di.ETLHelper;
import org.labkey.test.util.Ext4Helper;
import org.labkey.test.util.PipelineStatusTable;
import org.labkey.test.util.RReportHelper;
import org.labkey.test.util.RemoteConnectionHelper;
import org.labkey.test.util.SqlserverOnlyTest;
import org.labkey.test.util.di.DataIntegrationHelper;
import org.labkey.test.util.ehr.EHRClientAPIHelper;
import org.labkey.test.util.ehr.EHRTestHelper;

import java.io.File;
import java.net.URI;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
Expand All @@ -60,7 +52,7 @@
@Category({External.class, LabModule.class})
public class PMRTest extends BaseWebDriverTest implements SqlserverOnlyTest
{
private final ETLHelper _etlHelper = new ETLHelper(this, getProjectName());
private final DataIntegrationHelper _etlHelper = new DataIntegrationHelper(getProjectName());

@Override
protected void doCleanup(boolean afterTest) throws TestTimeoutException
Expand Down Expand Up @@ -158,7 +150,7 @@ private void testKinshipEtl() throws Exception
Assert.assertEquals("Incorrect number of kinship rows", 0, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue());

// Kick off ETL to stage data. This should also kick off a separate pipeline job to import, using geneticscore-importGeneticsData.view
_etlHelper.runETL("{PMR}/KinshipDataStaging");
_etlHelper.runTransform("{PMR}/KinshipDataStaging");
goToDataPipeline();
waitForPipelineJobsToComplete(4, "ETL Job: Import PRIMe-seq Kinship Data", false);

Expand Down