/*
* Copyright (C) 2012 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.pipeline.plugins;
import java.util.List;
import net.sourceforge.seqware.common.model.WorkflowRun;
import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator;
import static net.sourceforge.seqware.pipeline.plugins.PluginTest.metadata;
import org.apache.commons.dbutils.handlers.ArrayListHandler;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
/**
* Runs the tests for the FileLinker
*
* @author dyuen
*/
public class FileLinkerTest extends ExtendedPluginTest {
@BeforeClass
public static void beforeClass() {
BasicTestDatabaseCreator.resetDatabaseWithUsers();
}
@Before
@Override
public void setUp() {
instance = new FileLinker();
super.setUp();
}
public FileLinkerTest() {
}
@Test
public void testFileLinkerNormal() {
String path = FileLinkerTest.class.getResource("file_linker_test.txt").getPath();
launchPlugin("--workflow-accession", "4", "--file-list-file", path);
String s = getOut();
String firstWorkflowRun = getAndCheckSwid(s);
BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator();
List<Object[]> runQuery = dbCreator
.runQuery(
new ArrayListHandler(),
"select f.file_path, f.meta_type, i.sw_accession from workflow_run r, processing p, processing_files pf, file f, processing_ius pi, ius i\n"
+ "WHERE \n"
+ "r.sw_accession = ?\n"
+ "AND p.workflow_run_id = r.workflow_run_id\n"
+ "AND p.processing_id = pf.processing_id\n"
+ "AND pf.file_id = f.file_id\n"
+ "AND p.processing_id = pi.processing_id \n"
+ "AND pi.ius_id = i.ius_id\n"
+ "ORDER BY f.sw_accession\n"
+ "; ", Integer.valueOf(firstWorkflowRun));
Assert.assertTrue("first file values were incorrect",
runQuery.get(0)[0].equals("funky_file1.gz") && runQuery.get(0)[1].equals("txt"));
Assert.assertTrue("second file values were incorrect",
runQuery.get(1)[0].equals("funky_file2.gz") && runQuery.get(1)[1].equals("txt"));
Assert.assertTrue("ius links were correct", runQuery.get(0)[2].equals(4765) && runQuery.get(1)[2].equals(4765));
// check that we can get them back via metadata methods as well
WorkflowRun workflowRun = metadata.getWorkflowRunWithWorkflow(firstWorkflowRun);
Assert.assertTrue("could not retrieve optional fields via metadata",
workflowRun.getSwAccession().equals(Integer.valueOf(firstWorkflowRun)));
Assert.assertTrue("parent workflow incorrect", workflowRun.getWorkflow().getSwAccession() == 4);
String workflowRunReport = metadata.getWorkflowRunReport(Integer.valueOf(firstWorkflowRun));
// look for files using the gross metadata way
Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("funky_file1.gz")
&& workflowRunReport.contains("funky_file2.gz"));
s = s.split("\n")[1];
int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun);
Assert.assertTrue("second set of files could not be found using the metadata workflow run report",
workflowRunReport.contains("abc1.gz") && workflowRunReport.contains("abc2.gz"));
}
@Test
public void testFileLinkerComma() {
String path = FileLinkerTest.class.getResource("file_linker_test_comma.txt").getPath();
launchPlugin("--workflow-accession", "4", "--file-list-file", path, "--csv-separator", ",");
String s = getOut();
int firstWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
String workflowRunReport = metadata.getWorkflowRunReport(firstWorkflowRun);
// look for files using the gross metadata way
Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("cfunky_file1.gz")
&& workflowRunReport.contains("cfunky_file2.gz"));
s = s.split("\n")[1];
int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun);
Assert.assertTrue("second set of files could not be found using the metadata workflow run report",
workflowRunReport.contains("cabc1.gz") && workflowRunReport.contains("cabc2.gz"));
}
@Test
public void testFileLinkerWithNoLanes() {
String path = FileLinkerTest.class.getResource("file_linker_no_lane_test.txt").getPath();
launchPlugin("--workflow-accession", "4", "--file-list-file", path);
String s = getOut();
int firstWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
String workflowRunReport = metadata.getWorkflowRunReport(firstWorkflowRun);
// look for files using the gross metadata way
Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("nfunky_file1.gz")
&& workflowRunReport.contains("nfunky_file2.gz"));
s = s.split("\n")[1];
int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s));
workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun);
Assert.assertTrue("second set of files could not be found using the metadata workflow run report",
workflowRunReport.contains("nabc1.gz") && workflowRunReport.contains("nabc2.gz"));
}
@Test
public void checkRepeatedFileImportFail() {
String path = FileLinkerTest.class.getResource("file_linker_test2.txt").getPath();
launchPlugin("--workflow-accession", "4", "--file-list-file", path);
launchPlugin("--workflow-accession", "4", "--file-list-file", path);
// Test should already check for fail, check output after fixing logging
// String s = getOut();
// Assert.assertTrue("should be no file imports possible", s.contains("SWID") && StringUtils.countMatches(s, "Ignored file") == 4);
}
}