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DDP-5826-filling the kit history from files #187

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DDP-5826-filling the kit history from files #187

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0fd2997
Tool for migrating kits from file to db
pegahtah May 17, 2021
8781ebd
TestUnit for Testing that tool
pegahtah May 19, 2021
a1de833
Added fix for when one line has less kits that the other one
pegahtah May 19, 2021
47b33b7
Added more tests
pegahtah May 20, 2021
1cf3d00
Added more logging
pegahtah May 20, 2021
981d74a
Merge remote-tracking branch 'origin/develop' into HEAD
pegahtah May 20, 2021
d1ab551
Added more logging
pegahtah May 20, 2021
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188 changes: 188 additions & 0 deletions src/test/java/org/broadinstitute/dsm/UPSKitToolTest.java
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package org.broadinstitute.dsm;

import org.broadinstitute.dsm.db.DDPInstance;
import org.broadinstitute.dsm.util.DBTestUtil;
import org.broadinstitute.dsm.util.model.Kit;
import org.broadinstitute.dsm.util.tools.TbosUPSKitTool;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;

import java.util.ArrayList;
import java.util.Map;

import static org.broadinstitute.dsm.TestHelper.setupDB;
import static org.broadinstitute.dsm.util.tools.TbosUPSKitTool.readFile;

public class UPSKitToolTest {
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I made this class to test the methods I made in the migatioonTool

@Test
public void testDateConversion() {
String dateTimeStringInUTC = "2020-12-16T14:46:51Z";
String dateTimeStringInEST = TbosUPSKitTool.getSQLDateTimeString(dateTimeStringInUTC);
Assert.assertEquals(dateTimeStringInEST, "2020-12-16 09:46:51");
}

@Test
public void testKitSetValue() {
Kit kit = new Kit();
kit.setValueByHeader("kit label", "aaa");
Assert.assertEquals(kit.getKitLabel(), "aaa");
kit.setValueByHeader("reason", null);
Assert.assertEquals(kit.getReason(), null);
kit.setValueByHeader("result", "result1");
Assert.assertEquals(kit.getResult(), "result1");
kit.setValueByHeader("requested at", "2020-09-18T13:54:14.159Z");
Assert.assertEquals(kit.getRequestedAt(), "2020-09-18T13:54:14.159Z");
kit.setValueByHeader("shipped at", "2020-09-18T11:54:14.159Z");
Assert.assertEquals(kit.getShippedAt(), "2020-09-18T11:54:14.159Z");
kit.setValueByHeader("delivered at", "2020-09-15T11:54:14.159Z");
Assert.assertEquals(kit.getDeliveredAt(), "2020-09-15T11:54:14.159Z");
kit.setValueByHeader("picked up at", "2020-08-15T11:54:14.159Z");
Assert.assertEquals(kit.getPickedUpAt(), "2020-08-15T11:54:14.159Z");
kit.setValueByHeader("received at", "2020-08-15T12:54:14.159Z");
Assert.assertEquals(kit.getReceivedAt(), "2020-08-15T12:54:14.159Z");
kit.setValueByHeader("resulted at", "2019-08-15T12:54:14.159Z");
Assert.assertEquals(kit.getResultedAt(), "2019-08-15T12:54:14.159Z");
}

@Test
public void testReadFile() {
// String fileContent = TestUtil.readFile("NdiTestFile.txt");
Map<String, ArrayList<Kit>> participants = readFile("src/test/resources/TbosUPSKitToolTestFile.csv");
Assert.assertNotNull(participants);
Assert.assertEquals(participants.size(), 1);
Assert.assertTrue(participants.keySet().contains("TestBoston_PMVYGB"));
Assert.assertEquals(participants.get("TestBoston_PMVYGB").size(), 1);
ArrayList<Kit> ptKits = participants.get("TestBoston_PMVYGB");
Assert.assertEquals(ptKits.size(), 1);
Kit kit = ptKits.get(0);
Assert.assertEquals(kit.getKitLabel(), "TBOS-test");
Assert.assertNull(kit.getReason());
Assert.assertNull(kit.getResult());
}

@Test
public void testReadFileMultiPt() {
Map<String, ArrayList<Kit>> participants = readFile("src/test/resources/TbosUPSKitToolMultiPtKits.csv");
Assert.assertNotNull(participants);
Assert.assertEquals(participants.size(), 2);
Assert.assertTrue(participants.keySet().contains("TestBoston_PMVYGB"));
Assert.assertTrue(participants.keySet().contains("TestBoston_PBPD68"));
Assert.assertEquals(participants.get("TestBoston_PMVYGB").size(), 1);
Assert.assertEquals(participants.get("TestBoston_PBPD68").size(), 2);
ArrayList<Kit> ptKits = participants.get("TestBoston_PMVYGB");
Assert.assertEquals(ptKits.size(), 1);
Kit kit = ptKits.get(0);
Assert.assertEquals(kit.getKitLabel(), "TBOS-test");
Assert.assertNull(kit.getReason());
Assert.assertNull(kit.getResult());
ptKits = participants.get("TestBoston_PBPD68");
Assert.assertEquals(ptKits.size(), 2);
kit = ptKits.get(0);
Assert.assertEquals(kit.getKitLabel(), "TBOS-test4");
Assert.assertEquals(kit.getRequestedAt(), "2020-09-19T01:57:49Z");
Assert.assertNull(kit.getReason());
Assert.assertNull(kit.getResult());
kit = ptKits.get(1);
Assert.assertEquals(kit.getKitLabel(), "TBOS-test6");
Assert.assertEquals(kit.getRequestedAt(), "2020-09-22T10:57:49Z");
Assert.assertNull(kit.getReason());
Assert.assertNull(kit.getResult());
}


@Test
public void testGetDDPKitBasedOnKitLabel() {
DDPInstance ddpInstance = DDPInstance.getDDPInstance("testboston");
Kit outboundKit = TbosUPSKitTool.getDDBKitBasedOnKitLabel(TbosUPSKitTool.SQL_SELECT_KIT_BY_KIT_LABEL + TbosUPSKitTool.SQL_SELECT_OUTBOUND, "TBOS-test", ddpInstance.getDdpInstanceId());
Assert.assertNotNull(outboundKit);
Map<String, ArrayList<Kit>> participants = readFile("src/test/resources/TbosUPSKitToolTestFile.csv");
Assert.assertNotNull(participants);
Assert.assertEquals(participants.size(), 1);
Assert.assertTrue(participants.keySet().contains("TestBoston_PMVYGB"));
Assert.assertEquals(participants.get("TestBoston_PMVYGB").size(), 1);
ArrayList<Kit> ptKits = participants.get("TestBoston_PMVYGB");
Assert.assertEquals(ptKits.get(0).getGuid(), outboundKit.getGuid());
Assert.assertEquals(ptKits.get(0).getShortId(), outboundKit.getShortId());
Assert.assertEquals(ptKits.get(0).getKitLabel(), outboundKit.getKitLabel());
Assert.assertEquals("1Z9YA775YW21328147", outboundKit.getTrackingToId());
Assert.assertEquals("2309", outboundKit.getDsmKitRequestId());

Kit inboundKit = TbosUPSKitTool.getDDBKitBasedOnKitLabel(TbosUPSKitTool.SQL_SELECT_KIT_BY_KIT_LABEL + TbosUPSKitTool.SQL_SELECT_INBOUND, "TBOS-test", ddpInstance.getDdpInstanceId());
Assert.assertNotNull(inboundKit);
Assert.assertTrue(participants.keySet().contains("TestBoston_PMVYGB"));
Assert.assertEquals(participants.get("TestBoston_PMVYGB").size(), 1);
Assert.assertEquals(ptKits.get(0).getGuid(), inboundKit.getGuid());
Assert.assertEquals(ptKits.get(0).getShortId(), inboundKit.getShortId());
Assert.assertEquals(ptKits.get(0).getKitLabel(), inboundKit.getKitLabel());
Assert.assertEquals("92748902118533553033028108", inboundKit.getTrackingReturnId());
Assert.assertEquals("2309", outboundKit.getDsmKitRequestId());
}

@Test
public void testInsertShipment() {
Map<String, ArrayList<Kit>> participants = readFile("src/test/resources/TbosUPSKitToolMultiPtKits.csv");
Assert.assertNotNull(participants);
Assert.assertEquals(participants.size(), 2);
Assert.assertTrue(participants.keySet().contains("TestBoston_PMVYGB"));
Assert.assertTrue(participants.keySet().contains("TestBoston_PBPD68"));
Assert.assertEquals(participants.get("TestBoston_PMVYGB").size(), 1);
Assert.assertEquals(participants.get("TestBoston_PBPD68").size(), 2);
ArrayList<Kit> ptKits = participants.get("TestBoston_PMVYGB");
Assert.assertEquals(ptKits.size(), 1);
Kit kit = ptKits.get(0);
DDPInstance ddpInstance = DDPInstance.getDDPInstance("testboston");
Kit outboundKit = TbosUPSKitTool.getDDBKitBasedOnKitLabel(TbosUPSKitTool.SQL_SELECT_KIT_BY_KIT_LABEL + TbosUPSKitTool.SQL_SELECT_OUTBOUND, "TBOS-test", ddpInstance.getDdpInstanceId());
Assert.assertNotNull(outboundKit);
kit.setDsmKitRequestId(outboundKit.getDsmKitRequestId());
kit.setTrackingToId(outboundKit.getTrackingToId());
kit.setTrackingReturnId(outboundKit.getTrackingReturnId());
kit.setShipmentId(outboundKit.getShipmentId());
kit.setPackageId(outboundKit.getPackageId());
String shipmentId = TbosUPSKitTool.insertShipmentForKit(kit.getDsmKitRequestId());
kit.setShipmentId(shipmentId);
Assert.assertNotNull(shipmentId);
TbosUPSKitTool.insertPackagesForKit(kit);
String outboundPackage = TbosUPSKitTool.getPackageIdForKit(kit, false);
String inboundPackage = TbosUPSKitTool.getPackageIdForKit(kit, true);
Assert.assertNotNull(outboundPackage);
Assert.assertNotNull(inboundPackage);
Assert.assertNotEquals(inboundPackage, outboundPackage);
DBTestUtil.deleteFromQuery(shipmentId, "delete from ups_package where ups_shipment_id = ?");
DBTestUtil.deleteFromQuery(shipmentId, "delete from ups_shipment where ups_shipment_id = ?");
}

@Test
public void testTheBeforeFunction() {
Map<String, ArrayList<Kit>> participants = readFile("src/test/resources/TbosUPSKitToolMultiPtKits.csv");
Assert.assertNotNull(participants);
Assert.assertEquals(participants.size(), 2);
Assert.assertTrue(participants.keySet().contains("TestBoston_PBPD68"));
Assert.assertEquals(participants.get("TestBoston_PBPD68").size(), 2);
ArrayList<Kit> ptKits = participants.get("TestBoston_PBPD68");
Assert.assertEquals(ptKits.size(), 2);
Kit kit = ptKits.get(1);
DDPInstance ddpInstance = DDPInstance.getDDPInstance("testboston");
Kit dbKit = TbosUPSKitTool.getDDBKitBasedOnKitLabel(TbosUPSKitTool.SQL_SELECT_KIT_BY_KIT_LABEL + TbosUPSKitTool.SQL_SELECT_OUTBOUND, kit.getKitLabel(), ddpInstance.getDdpInstanceId());
Assert.assertEquals( "2021-04-22 14:22:00", dbKit.getLastActivityDateTime());
Assert.assertEquals( "2021-04-19T21:38:31Z", kit.getShippedAt());
boolean b = TbosUPSKitTool.shouldInsertBasedOnTimeForKit(dbKit, kit.getShippedAt());
Assert.assertFalse(b);
}


@BeforeClass
public static void first() {
setupDB();
}

@Ignore
@Test
public void InsertFile() {
Map<String, ArrayList<Kit>> participants = TbosUPSKitTool.readFile("src/test/resources/TbosUPSKitToolTestFile.csv");
TbosUPSKitTool.insertFileInfo(participants);
}


}
117 changes: 117 additions & 0 deletions src/test/java/org/broadinstitute/dsm/util/model/Kit.java
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package org.broadinstitute.dsm.util.model;

import lombok.Data;
import org.apache.commons.lang3.StringUtils;

@Data
public class Kit {

String kitLabel;
String reason;
String result;
String requestedAt;
String shippedAt;
String deliveredAt;
String pickedUpAt;
String receivedAt;
String resultedAt;
String dsmKitRequestId;
String trackingToId;
String trackingReturnId;
String lastActivityDateTime;
String lastActivityDesc;
String shipmentId;
String packageId;
String shortId;
String guid;

public Kit() {
}

public Kit(String kitLabel,
String reason,
String result,
String requestedAt,
String shippedAt,
String deliveredAt,
String pickedUpAt,
String receivedAt,
String resultedAt,
String dsmKitRequestId,
String trackingToId,
String trackingReturnId,
String lastActivityDateTime,
String lastActivityDesc,
String shipmentId,
String packageId,
String shortId,
String guid) {
this.kitLabel = kitLabel;
this.reason = reason;
this.result = result;
this.requestedAt = requestedAt;
this.shippedAt = shippedAt;
this.deliveredAt = deliveredAt;
this.pickedUpAt = pickedUpAt;
this.receivedAt = receivedAt;
this.resultedAt = resultedAt;
this.dsmKitRequestId = dsmKitRequestId;
this.trackingToId = trackingToId;
this.trackingReturnId = trackingReturnId;
this.lastActivityDateTime = lastActivityDateTime;
this.lastActivityDesc = lastActivityDesc;
this.shipmentId = shipmentId;
this.packageId = packageId;
this.shortId = shortId;
this.guid = guid;
}

public void setValueByHeader(String header, String value) {
switch (header) {
case "kit label":
this.kitLabel = value;
break;
case "reason":
this.reason = value;
break;
case "result":
this.result = value;
break;
case "requested at":
this.requestedAt = value;
break;
case "shipped at":
this.shippedAt = value;
break;
case "delivered at":
this.deliveredAt = value;
break;
case "picked up at":
this.pickedUpAt = value;
break;
case "received at":
this.receivedAt = value;
break;
case "resulted at":
this.resultedAt = value;
break;
default:
throw new IllegalStateException("Unexpected header, value: " + header + "," + value);
}
}

public boolean isEmpty() {
if (StringUtils.isBlank(kitLabel) &&
StringUtils.isBlank(reason) &&
StringUtils.isBlank(result) &&
StringUtils.isBlank(requestedAt) &&
StringUtils.isBlank(shippedAt) &&
StringUtils.isBlank(deliveredAt) &&
StringUtils.isBlank(pickedUpAt) &&
StringUtils.isBlank(receivedAt) &&
StringUtils.isBlank(resultedAt)){
return true;
}
return false;
}
}
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