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The client-side library for Java developers is a separate JAR from the LabKey Server code base. It can be used by any Java program, including another Java web application.
/*
* Copyright (c) 2008-2016 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.labkey.remoteapi.test;
import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.Connection;
import org.labkey.remoteapi.assay.AssayListCommand;
import org.labkey.remoteapi.assay.AssayListResponse;
import org.labkey.remoteapi.assay.nab.NAbRunsCommand;
import org.labkey.remoteapi.assay.nab.NAbRunsResponse;
import org.labkey.remoteapi.assay.nab.model.NAbNeutralizationResult;
import org.labkey.remoteapi.assay.nab.model.NAbRun;
import org.labkey.remoteapi.assay.nab.model.NAbSample;
import org.labkey.remoteapi.query.ContainerFilter;
import org.labkey.remoteapi.query.DeleteRowsCommand;
import org.labkey.remoteapi.query.ExecuteSqlCommand;
import org.labkey.remoteapi.query.Filter;
import org.labkey.remoteapi.query.GetQueriesCommand;
import org.labkey.remoteapi.query.GetQueriesResponse;
import org.labkey.remoteapi.query.GetSchemasCommand;
import org.labkey.remoteapi.query.GetSchemasResponse;
import org.labkey.remoteapi.query.InsertRowsCommand;
import org.labkey.remoteapi.query.SaveRowsResponse;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.remoteapi.query.SelectRowsResponse;
import org.labkey.remoteapi.query.Sort;
import org.labkey.remoteapi.query.TruncateTableCommand;
import org.labkey.remoteapi.query.TruncateTableResponse;
import org.labkey.remoteapi.query.UpdateRowsCommand;
import java.io.IOException;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class Test
{
private static final String LIST_FOLDER = "Api Test";
private static final String STUDY_FOLDER = "StudyVerifyProject/My Study";
private static final String NAB_FOLDER = "/Nab Test Verify Project/nabassay";
public static void main(String[] args) throws Exception
{
String baseUrl = "http://localhost:8080/labkey";
Connection cn = args.length < 2 ? new Connection(baseUrl) : new Connection(baseUrl, args[0], args[1]);
//Connection cn = new Connection(baseUrl, new ApiKeyCredentialsProvider("session:d7c3a4aeb283e3e54c4126a707908420"));
//Connection cn = new Connection(baseUrl, new NetRcCredentialsProvider(baseUrl));
try
{
// Import /remoteapi/labkey-api-java/People.xls as list "People" into project "Api Test"
selectTest(cn, LIST_FOLDER);
crudTest(cn, LIST_FOLDER);
execSqlTest(cn, LIST_FOLDER);
schemasTest(cn, LIST_FOLDER);
extendedFormatTest(cn, LIST_FOLDER);
// Run ShortStudyTest with -Dclean=false
datasetTest(cn, STUDY_FOLDER);
// Run NabAssayTest with -Dclean=false and rename subfolder "Rename############" to "nabassay"
nabTest(cn, NAB_FOLDER);
assayTest(cn, NAB_FOLDER);
truncateAssayFailsTest(cn, NAB_FOLDER);
truncateTableSuccessTest(cn, LIST_FOLDER);
System.out.println("*** All tests completed successfully ***");
}
catch(CommandException e)
{
e.printStackTrace();
}
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
public static void selectTest(Connection cn, String folder) throws Exception
{
SelectRowsCommand cmd = new SelectRowsCommand("lists", "People");
cmd.addSort(new Sort("Last"));
cmd.getColumns().add("First");
cmd.getColumns().add("Last");
SelectRowsResponse response = cmd.execute(cn, folder);
System.out.println("Number of rows: " + response.getRowCount());
List> rows = response.getRows();
for (Map row : rows)
{
System.out.println(row);
}
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
public static void crudTest(Connection cn, String folder) throws Exception
{
int rowCount = 0;
//get the current row count
SelectRowsCommand cmdsel = new SelectRowsCommand("lists", "People");
SelectRowsResponse srresp = cmdsel.execute(cn, folder);
rowCount = srresp.getRowCount().intValue();
//insert a row
InsertRowsCommand cmdins = new InsertRowsCommand("lists", "People");
Map row = new HashMap();
row.put("First", "To Be Inserted");
row.put("Last", "Test Inserted Value");
cmdins.addRow(row);
SaveRowsResponse resp = cmdins.execute(cn, folder);
//make sure row count is one greater
srresp = cmdsel.execute(cn, folder);
assert srresp.getRowCount().intValue() == rowCount + 1;
assert srresp.getRows().get(srresp.getRows().size() - 1).get("First").equals("To Be Inserted");
//update the newly-added row
UpdateRowsCommand cmdupd = new UpdateRowsCommand("lists", "People");
row = resp.getRows().get(resp.getRows().size() - 1);
row.put("LastName", "Test UPDATED");
cmdupd.addRow(row);
resp = cmdupd.execute(cn, folder);
assert resp.getRowsAffected().intValue() == 1;
assert resp.getRows().get(resp.getRows().size() - 1).get("Last").equals("Test UPDATED");
//delete the newly added row
DeleteRowsCommand cmddel = new DeleteRowsCommand("lists", "People");
cmddel.addRow(row);
resp = cmddel.execute(cn, folder);
assert resp.getRowsAffected().intValue() == 1;
//assert that the row count is back to what it was
srresp = cmdsel.execute(cn, folder);
assert srresp.getRowCount().intValue() == rowCount;
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
public static void truncateTableSuccessTest(Connection cn, String folder) throws Exception
{
TruncateTableCommand trunc = new TruncateTableCommand("lists", "People");
TruncateTableResponse resp = trunc.execute(cn, folder);
assert resp.getDeletedRowCount() == 9;
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
public static void execSqlTest(Connection cn, String folder) throws Exception
{
ExecuteSqlCommand cmd = new ExecuteSqlCommand("lists");
cmd.setSql("SELECT Last, COUNT(*) AS Num FROM People GROUP BY Last");
SelectRowsResponse resp = cmd.execute(cn, folder);
System.out.println(resp.getRows());
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
private static void schemasTest(Connection cn, String folder) throws Exception
{
GetSchemasCommand cmd = new GetSchemasCommand();
GetSchemasResponse resp = cmd.execute(cn, folder);
for (String name : resp.getSchemaNames())
{
System.out.println(name);
}
GetQueriesCommand cmdq = new GetQueriesCommand("lists");
GetQueriesResponse respq = cmdq.execute(cn, folder);
for (String qname : respq.getQueryNames())
{
System.out.println(qname);
for (String colName : respq.getColumnNames(qname))
{
System.out.println(" " + colName);
}
}
}
// Assumes that /remoteapi/labkey-api-java/People.xls has been imported as a list into folder
private static void extendedFormatTest(Connection cn, String folder) throws Exception
{
SelectRowsCommand cmd = new SelectRowsCommand("lists", "People");
cmd.setRequiredVersion(9.1);
SelectRowsResponse resp = cmd.execute(cn, folder);
for (Map row : resp.getRows())
{
for (Map.Entry entry : row.entrySet())
{
Object value = ((Map)entry.getValue()).get("value");
System.out.println(entry.getKey() + " = " + value + " (type: " + (null == value ? "null" : value.getClass().getName()) + ")");
}
}
}
// Assumes StudyShortTest has been run with -Dclean=false
public static void datasetTest(Connection cn, String folder) throws Exception
{
SelectRowsCommand select = new SelectRowsCommand("study", "DataSets");
SelectRowsResponse response = select.execute(cn, folder);
List> rows = response.getRows();
for (Map row : rows)
System.out.println(row);
for (String queryName : new String[]{"DEM-1", "DEM-1: Demographics"})
{
SelectRowsCommand datasetRowSelect = new SelectRowsCommand("study", queryName);
datasetRowSelect.addFilter(new Filter("MouseId", "999320565"));
SelectRowsResponse datasetRow = datasetRowSelect.execute(cn, folder);
Map row = datasetRow.getRows().get(0);
System.out.println(row);
if (!row.get("DEMracox").equals("Brazilian"))
throw new RuntimeException("Race is not 'Brazilian' before update");
UpdateRowsCommand update = new UpdateRowsCommand("study", queryName);
row.put("DEMracox", "Martian");
update.setRows(Collections.singletonList(row));
update.execute(cn, "StudyVerifyProject/My Study");
datasetRowSelect = new SelectRowsCommand("study", queryName);
datasetRowSelect.addFilter(new Filter("MouseId", "999320565"));
datasetRow = datasetRowSelect.execute(cn, "StudyVerifyProject/My Study");
row = datasetRow.getRows().get(0);
System.out.println(row);
if (!row.get("DEMracox").equals("Martian"))
throw new RuntimeException("Race is not 'Martian' after first update");
update = new UpdateRowsCommand("study", queryName);
row.put("DEMracox", "Brazilian");
update.setRows(Collections.singletonList(row));
update.execute(cn, "StudyVerifyProject/My Study");
datasetRowSelect = new SelectRowsCommand("study", queryName);
datasetRowSelect.addFilter(new Filter("MouseId", "999320565"));
datasetRow = datasetRowSelect.execute(cn, "StudyVerifyProject/My Study");
row = datasetRow.getRows().get(0);
System.out.println(row);
if (!row.get("DEMracox").equals("Brazilian"))
throw new RuntimeException("Race is not 'Brazilian' after second update");
}
}
// Assumes that NabAssayTest has been run with -Dclean=false
public static void nabTest(Connection cn, String folder) throws Exception
{
double avg = getAverageNeutralization(cn, folder, "TestAssayNab", 50);
}
public static double getAverageNeutralization(Connection cn, String folderPath, String assayName, int cutoff) throws CommandException, IOException
{
NAbRunsCommand nabCommand = new NAbRunsCommand();
nabCommand.setContainerFilter(ContainerFilter.CurrentAndSubfolders);
nabCommand.setAssayName(assayName);
nabCommand.setCalculateNeut(true);
nabCommand.setIncludeFitParameters(false);
nabCommand.setIncludeStats(false);
nabCommand.setIncludeWells(false);
// nabCommand.addFilter(new Filter("Name", "m0902051", Filter.Operator.STARTS_WITH));
nabCommand.addSort(new Sort("VirusName", Sort.Direction.ASCENDING));
NAbRunsResponse runResponse = nabCommand.execute(cn, folderPath);
NAbRun[] runs = runResponse.getRuns();
int totalSamples = 0;
double totalIC50CurveNeutralization = 0;
for (NAbRun run : runs)
{
for (NAbSample sample : run.getSamples())
{
long objectId = sample.getObjectId();
for (NAbNeutralizationResult neutResult : sample.getNeutralizationResults())
{
// only total non-infinite values (that is, results where we found a neutralizing dilution:
if (neutResult.getCutoff() == cutoff && !Double.isInfinite(neutResult.getCurveBasedDilution()))
{
totalSamples++;
totalIC50CurveNeutralization += neutResult.getCurveBasedDilution();
}
}
}
}
return totalIC50CurveNeutralization/totalSamples;
}
// Assumes that folder has been populated with assays
public static void assayTest(Connection cn, String folder) throws Exception
{
AssayListCommand cmd = new AssayListCommand();
AssayListResponse resp = cmd.execute(cn, folder);
System.out.println(resp.getDefinitions());
}
// Assumes that folder has been populated with assays
public static void truncateAssayFailsTest(Connection cn, String folder) throws Exception
{
TruncateTableCommand trunc = new TruncateTableCommand("assay.NAb.TestAssayNab", "WellData");
try
{
TruncateTableResponse resp = trunc.execute(cn, folder);
throw new RuntimeException("Truncate table command should not succeed for tables other than lists," +
"datasets, sample sets, data classes, and issues");
}
catch (CommandException e)
{
assert e.getStatusCode() == 500;
assert e.getLocalizedMessage().equals("The query 'WellData' in the schema 'assay.NAb.TestAssayNab' is not truncatable.");
}
}
}