Java tutorial
/* * 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.deciders; import com.google.gson.Gson; import com.google.gson.GsonBuilder; import com.google.gson.reflect.TypeToken; import io.seqware.Reports; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; import java.io.PrintStream; import java.lang.reflect.Type; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeMap; import net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header; import net.sourceforge.seqware.common.metadata.MetadataWS; import net.sourceforge.seqware.common.model.ExperimentAttribute; import net.sourceforge.seqware.common.model.FileAttribute; import net.sourceforge.seqware.common.model.IUSAttribute; import net.sourceforge.seqware.common.model.LaneAttribute; import net.sourceforge.seqware.common.model.ProcessingAttribute; import net.sourceforge.seqware.common.model.SampleAttribute; import net.sourceforge.seqware.common.model.SequencerRunAttribute; import net.sourceforge.seqware.common.model.StudyAttribute; import net.sourceforge.seqware.common.module.FileMetadata; import net.sourceforge.seqware.common.module.ReturnValue; import net.sourceforge.seqware.common.util.Log; import net.sourceforge.seqware.common.util.maptools.ReservedIniKeys; import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator; import net.sourceforge.seqware.pipeline.plugins.PluginTest; import org.apache.commons.io.FileUtils; import org.junit.*; /** * <p>BasicDeciderTest class.</p> * * @author boconnor, dyuen * @version $Id: $Id * @since 0.13.3 */ public class BasicDeciderTest extends PluginTest { /** * Write JSON representations of Attributes map so that we can ensure * that deciders are given a superset of attributes for backwards compatibility */ private static final boolean WRITE_JSON_ATTRIBUTES = false; private final List<String> fastq_gz = new ArrayList<>(); private final BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); @BeforeClass public static void beforeClass() { BasicTestDatabaseCreator.resetDatabaseWithUsers(); Reports.triggerProvenanceReport(); } @Before @Override public void setUp() { super.setUp(); instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); fastq_gz.add("chemical/seq-na-fastq-gzip"); } @Test public void testIsWorkflowRunWithFailureStatus() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); boolean pendingStatus = decider.determineStatus( metadata.getWorkflowRun(6602).getStatus()) == BasicDecider.PREVIOUS_RUN_STATUS.OTHER; boolean failedStatus = decider.determineStatus( metadata.getWorkflowRun(6603).getStatus()) == BasicDecider.PREVIOUS_RUN_STATUS.FAILED; boolean completedStatus = decider.determineStatus( metadata.getWorkflowRun(6604).getStatus()) == BasicDecider.PREVIOUS_RUN_STATUS.COMPLETED; Assert.assertTrue("pending status was not false", pendingStatus == true); Assert.assertTrue("failed status was not true", failedStatus == true); Assert.assertTrue("completed status was not false", completedStatus == true); } @Test public void testListAllFiles() { // we need to use a valid workflow now that we filter with valid parent workflows // this is actually a bit misnamed, we return all files that are associated with all studies String[] params = { "--all", "--wf-accession", "4773", "--parent-wf-accessions", "2861,4767,4768,4769,4773,4780,4778,4775,4774,5692,6594,6595,6596,6597,6598,6599,6685,6692,2860,4", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 80); } @Test public void testFilesForOneStudy() { String[] params = { "--study-name", "AbcCo_Exome_Sequencing", "--wf-accession", "4773", "--parent-wf-accessions", "2861,4767,4768,4769,4773,4780,4778,4775,4774,5692,6594,6595,6596,6597,6598,6599,6685,6692,2860", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 17); } @Test public void testFilesForOneSample() { String[] params = { "--sample-name", "Exome_ABC015069_Test_2", "--wf-accession", "4773", "--parent-wf-accessions", "2861,4767,4768,4769,4773,4780,4778,4775,4774,5692,6594,6595,6596,6597,6598,6599,6685,6692,2860", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 17); } @Test public void testFilesForOneSequencerRun() { String[] params = { "--sequencer-run-name", "SRKDKJKLFJKLJ90039", "--wf-accession", "4773", "--parent-wf-accessions", "2861,4767,4768,4769,4773,4780,4778,4775,4774,5692,6594,6595,6596,6597,6598,6599,6685,6692,2860", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 32); } @Test public void testNumberOfChecks() { String[] params = { "--all", "--wf-accession", "6685", "--parent-wf-accessions", "4767", "--test" }; launchAndCaptureOutput(params); //int launchesDetected = StringUtils.countMatches(redirected, "java -jar"); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 3); // we expect to launch 3 times Assert.assertTrue( "output does not contain the correct number of launches, we saw " + decider.getFinalChecks(), decider.getFinalChecks() == 3); } @Test public void testNumberOfChecksForAllFileTypes() { String[] params = { "--all", "--wf-accession", "4773", "--meta-types", "text/h-tumour,application/vcf-4-gzip,text/annovar-tags,application/zip-report-bundle,txt,chemical/seq-na-fastq-gzip,application/bam,text/vcf-4,chemical/seq-na-fastq", "--test" }; launchAndCaptureOutput(params); //int launchesDetected = StringUtils.countMatches(redirected, "java -jar"); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 80); // we expect to launch 3 times Assert.assertTrue( "output does not contain the correct number of launches, we saw " + decider.getFinalChecks(), decider.getFinalChecks() == 80); } @Test public void testFinalCheckFailure() { // swap out the decider instance = new AlwaysBlockFinalCheckDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); // a AlwaysBlockFinalCheckDecider decider should never launch String[] params = { "--all", "--wf-accession", "6685", "--parent-wf-accessions", "4767", "--ignore-previous-runs", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 3); // we expect to never launch with the halting decider Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 0); // swap back the decider instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); } @Test public void testIgnorePreviousRuns() { // swap out the decider instance = new HaltingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); // a halting decider should launch twice after denying one launch String[] params = { "--all", "--wf-accession", "6685", "--parent-wf-accessions", "4767", "--ignore-previous-runs", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 3); // we expect to never launch with the halting decider Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 2); // swap back the decider instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); } @Test public void testSEQWARE1298() { // swap out the decider instance = new HaltingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); // a halting decider should launch twice after denying one launch String[] params = { "--all", "--wf-accession", "6685", "--parent-wf-accessions", "4767", "--test" }; launchAndCaptureOutput(params); // we need to override handleGroupByAttribute in order to count the number of expected files TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total, this changes due to file provenance report Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 3); // we expect to launch exactly twice Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 2); // swap back the decider instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); } @Test public void testMetaTypes() { String[] params = { "--all", "--wf-accession", "4773", "--meta-types", "application/bam,text/vcf-4,chemical/seq-na-fastq-gzip", "--test" }; launchAndCaptureOutput(params); TestingDecider decider = (TestingDecider) instance; // we expect to see 133 files in total Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 80); Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 61); } @Test public void testSEQWARE1297DoNotLaunchProcessingWorkflows() { String[] params = { "--sample", "Sample_Tumour", "--wf-accession", "2860", "--meta-types", "application/bam,text/vcf-4,chemical/seq-na-fastq-gzip", "--test" }; launchAndCaptureOutput(params); TestingDecider decider = (TestingDecider) instance; Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 15); Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 12); } @Test public void testSEQWARE1297DoNotLaunchFailedWorkflows() { // trying to find a good test for this, doesn't look like there is one in the testing database? // there is one pending workflow_run as revealed by "select * from workflow_run WHERE status = 'pending';" // however, it doesn't appear to be properly linked in // see "select sh.*, s.* FROM sample_hierarchy sh , (select DISTINCT s.sample_id from workflow_run wr, ius_workflow_runs iwr, ius, sample s WHERE status = 'pending' AND wr.workflow_run_id=iwr.workflow_run_id AND iwr.ius_id=ius.ius_id AND ius.sample_id=s.sample_id) sq, sample s WHERE sh.sample_id=sq.sample_id AND s.sample_id=sh.parent_id;" String[] params = new String[] { "--sample", "", "--wf-accession", "4773", "--meta-types", "application/bam,text/vcf-4,chemical/seq-na-fastq-gzip", "--rerun-max", "10", "--test" }; launchAndCaptureOutput(params); TestingDecider decider = (TestingDecider) instance; Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 47); Assert.assertTrue("output does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 36); params = new String[] { "--sample", "", "--wf-accession", "4773", "--meta-types", "application/bam,text/vcf-4,chemical/seq-na-fastq-gzip", "--rerun-max", "1", "--test" }; launchAndCaptureOutput(params); Assert.assertTrue("output 2 does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 47); Assert.assertTrue( "output 2 does not contain the correct number of launches, we saw " + decider.getLaunches(), decider.getLaunches() == 34); } @Test public void testDecidingWithAttributes() { // swap out the decider instance = new AttributeCheckingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); AttributeCheckingDecider decider = (AttributeCheckingDecider) instance; // create a hierarchy so that we can check for parent samples dbCreator.runUpdate("insert into sample_hierarchy VALUES(11,12);"); // create attributes on all relevant columns StudyAttribute studyAttribute = new StudyAttribute(); studyAttribute.setTag("studyTag"); studyAttribute.setValue("studyValue"); metadata.annotateStudy(120, studyAttribute, false); ExperimentAttribute experimentAttribute = new ExperimentAttribute(); experimentAttribute.setTag("experimentTag"); experimentAttribute.setValue("experimentValue"); metadata.annotateExperiment(4782, experimentAttribute, false); SampleAttribute sampleAttribute = new SampleAttribute(); sampleAttribute.setTag("sampleTag"); sampleAttribute.setValue("sampleValue"); metadata.annotateSample(4783, sampleAttribute, false); SampleAttribute parentSampleAttribute = new SampleAttribute(); parentSampleAttribute.setTag("parentSampleTag"); parentSampleAttribute.setValue("parentSampleValue"); metadata.annotateSample(6158, parentSampleAttribute, false); SequencerRunAttribute sequencerRunAttribute = new SequencerRunAttribute(); sequencerRunAttribute.setTag("sequencerRunTag"); sequencerRunAttribute.setValue("sequencerRunValue"); metadata.annotateSequencerRun(4715, sequencerRunAttribute, false); metadata.annotateSequencerRun(47150, sequencerRunAttribute, false); LaneAttribute laneAttribute = new LaneAttribute(); laneAttribute.setTag("laneTag"); laneAttribute.setValue("laneValue"); metadata.annotateLane(6105, laneAttribute, false); metadata.annotateLane(4788, laneAttribute, false); IUSAttribute iusAttribute = new IUSAttribute(); iusAttribute.setTag("iusTag"); iusAttribute.setValue("iusValue"); metadata.annotateIUS(6106, iusAttribute, false); metadata.annotateIUS(4789, iusAttribute, false); ProcessingAttribute processingAttribute = new ProcessingAttribute(); processingAttribute.setTag("processingTag"); processingAttribute.setValue("processingValue"); metadata.annotateProcessing(6104, processingAttribute, false); metadata.annotateProcessing(6063, processingAttribute, false); metadata.annotateProcessing(5988, processingAttribute, false); metadata.annotateProcessing(5981, processingAttribute, false); metadata.annotateProcessing(5978, processingAttribute, false); metadata.annotateProcessing(5876, processingAttribute, false); metadata.annotateProcessing(5873, processingAttribute, false); metadata.annotateProcessing(5868, processingAttribute, false); metadata.annotateProcessing(5166, processingAttribute, false); metadata.annotateProcessing(4821, processingAttribute, false); metadata.annotateProcessing(4787, processingAttribute, false); FileAttribute fileAttribute = new FileAttribute(); fileAttribute.setTag("fileTag"); fileAttribute.setValue("fileValue"); metadata.annotateFile(6103, fileAttribute, false); metadata.annotateFile(6102, fileAttribute, false); metadata.annotateFile(6064, fileAttribute, false); metadata.annotateFile(6065, fileAttribute, false); metadata.annotateFile(6066, fileAttribute, false); metadata.annotateFile(6067, fileAttribute, false); metadata.annotateFile(5989, fileAttribute, false); metadata.annotateFile(5990, fileAttribute, false); metadata.annotateFile(5986, fileAttribute, false); metadata.annotateFile(5979, fileAttribute, false); metadata.annotateFile(5877, fileAttribute, false); metadata.annotateFile(5878, fileAttribute, false); metadata.annotateFile(5874, fileAttribute, false); metadata.annotateFile(5869, fileAttribute, false); metadata.annotateFile(5167, fileAttribute, false); metadata.annotateFile(4822, fileAttribute, false); metadata.annotateFile(4823, fileAttribute, false); metadata.annotateFile(4824, fileAttribute, false); metadata.annotateFile(4825, fileAttribute, false); metadata.annotateFile(4786, fileAttribute, false); metadata.annotateFile(4785, fileAttribute, false); // in this version of deciders, we need to refresh the report Reports.triggerProvenanceReport(); // run decider and check that attributes are pulled back properly String[] params = { "--study-name", "AbcCo_Exome_Sequencing", "--wf-accession", "4", "--meta-types", "text/h-tumour,application/vcf-4-gzip,text/annovar-tags,application/zip-report-bundle,txt,chemical/seq-na-fastq-gzip,application/bam,text/vcf-4,chemical/seq-na-fastq", "--test" }; launchAndCaptureOutput(params); Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 17); Assert.assertTrue("we didn't check the correct number of files, we checked " + decider.filesChecked, decider.filesChecked == 17); // swap back the decider instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); } @Test public void testDecidingWithFilemetadata() { // swap out the decider instance = new FileMetadataDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); FileMetadataDecider decider = (FileMetadataDecider) instance; //update the database so targetted files will contain full metadata dbCreator.runUpdate( "update file set md5sum = sw_accession + 42 WHERE sw_accession IN (SELECT file_swa from file_provenance_report WHERE study_swa=120);"); dbCreator.runUpdate( "update file set description = 'funky_description' WHERE sw_accession IN (SELECT file_swa from file_provenance_report WHERE study_swa=120);"); dbCreator.runUpdate( "update file set size = sw_accession + 1701 WHERE sw_accession IN (SELECT file_swa from file_provenance_report WHERE study_swa=120);"); // in this version of deciders, we need to refresh the report Reports.triggerProvenanceReport(); // use a special decider to ensure that filemetadata is populated String[] params = { "--study-name", "AbcCo_Exome_Sequencing", "--wf-accession", "4", "--meta-types", "text/h-tumour,application/vcf-4-gzip,text/annovar-tags,application/zip-report-bundle,txt,chemical/seq-na-fastq-gzip,application/bam,text/vcf-4,chemical/seq-na-fastq", "--test" }; launchAndCaptureOutput(params); Assert.assertTrue("output does not contain the correct number of files, we saw " + decider.getFileCount(), decider.getFileCount() == 17); Assert.assertTrue("we didn't check the correct number of files, we checked " + decider.filesChecked, decider.filesChecked == 17); // swap back the decider instance = new TestingDecider(); //instance = new BasicDecider(); instance.setMetadata(metadata); } public class AlwaysBlockFinalCheckDecider extends TestingDecider { @Override protected ReturnValue doFinalCheck(String commaSeparatedFilePaths, String commaSeparatedParentAccessions) { return new ReturnValue(ReturnValue.FAILURE); } } public class HaltingDecider extends TestingDecider { boolean haltedOnce = false; @Override protected ReturnValue doFinalCheck(String commaSeparatedFilePaths, String commaSeparatedParentAccessions) { super.doFinalCheck(commaSeparatedFilePaths, commaSeparatedParentAccessions); ReturnValue localRet; if (!haltedOnce) { haltedOnce = true; localRet = new ReturnValue(ReturnValue.FAILURE); } else { localRet = new ReturnValue(ReturnValue.SUCCESS); } return localRet; } } public class AttributeCheckingDecider extends TestingDecider { int filesChecked = 0; @Override protected boolean checkFileDetails(ReturnValue returnValue, FileMetadata fm) { filesChecked++; int file_swa = Integer.valueOf(returnValue.getAttribute(Header.FILE_SWA.getTitle())); try { String attribute = returnValue.getAttribute(Header.STUDY_TAG_PREFIX.getTitle() + "studyTag"); Assert.assertTrue("studyTag attribute didn't make it for " + file_swa, attribute.equals("studyValue")); attribute = returnValue.getAttribute(Header.EXPERIMENT_TAG_PREFIX.getTitle() + "experimentTag"); Assert.assertTrue("experimentTag attribute didn't make it for " + file_swa, attribute.equals("experimentValue")); attribute = returnValue .getAttribute(Header.PARENT_SAMPLE_TAG_PREFIX.getTitle() + "parentSampleTag.6158"); Assert.assertTrue("parentSampleTag attribute didn't make it for " + file_swa, attribute.equals("parentSampleValue")); attribute = returnValue.getAttribute(Header.SAMPLE_TAG_PREFIX.getTitle() + "sampleTag"); Assert.assertTrue("sampleTag attribute didn't make it for " + file_swa, attribute.equals("sampleValue")); attribute = returnValue .getAttribute(Header.SEQUENCER_RUN_TAG_PREFIX.getTitle() + "sequencerRunTag"); Assert.assertTrue("sequencerRunTag attribute didn't make it for " + file_swa, attribute.equals("sequencerRunValue")); attribute = returnValue.getAttribute(Header.LANE_TAG_PREFIX.getTitle() + "laneTag"); Assert.assertTrue("lane attribute didn't make it for " + file_swa, attribute.equals("laneValue")); attribute = returnValue.getAttribute(Header.IUS_TAG_PREFIX.getTitle() + "iusTag"); Assert.assertTrue("ius attribute didn't make it for " + file_swa, attribute.equals("iusValue")); attribute = returnValue.getAttribute(Header.PROCESSING_TAG_PREFIX.getTitle() + "processingTag"); Assert.assertTrue("processing attribute didn't make it for " + file_swa, attribute.equals("processingValue")); attribute = returnValue.getAttribute(Header.FILE_TAG_PREFIX.getTitle() + "fileTag"); Assert.assertTrue("file attribute didn't make it for " + file_swa, attribute.equals("fileValue")); } catch (NullPointerException ex) { Assert.assertTrue("returnvalue attributes missing: " + returnValue.getAttributes().toString(), false); } try { if (BasicDeciderTest.WRITE_JSON_ATTRIBUTES) { Gson gson = new GsonBuilder().create(); String toJson = gson.toJson(returnValue.getAttributes()); File file = new File(file_swa + ".json"); FileUtils.writeStringToFile(file, toJson); } else { //ensure that json check files contain a subset of the decider attributes String query = FileUtils.readFileToString( new File((BasicDeciderTest.class.getResource(file_swa + ".json").getPath()))); Gson gson = new GsonBuilder().create(); Type fooType = new TypeToken<Map<String, String>>() { }.getType(); Map<String, String> oldAttributes = gson.fromJson(query, fooType); // remove last modified time from both since time changes when annotating oldAttributes.remove(Header.PROCESSING_DATE.getTitle()); returnValue.getAttributes().remove(Header.PROCESSING_DATE.getTitle()); boolean contained = returnValue.getAttributes().entrySet() .containsAll(oldAttributes.entrySet()); if (!contained) { String oldStr = oldAttributes.toString(); String newStr = returnValue.getAttributes().toString(); oldAttributes.entrySet().removeAll(returnValue.getAttributes().entrySet()); String diff = oldAttributes.toString(); Assert.assertTrue( "old returnvalue is not a subset: " + oldStr + "\n" + newStr + "\n" + diff, false); } } } catch (IOException ex) { throw new RuntimeException(ex); } return false; } } public class FileMetadataDecider extends TestingDecider { int filesChecked = 0; @Override protected boolean checkFileDetails(ReturnValue returnValue, FileMetadata fm) { filesChecked++; int file_swa = Integer.valueOf(returnValue.getAttribute(Header.FILE_SWA.getTitle())); Assert.assertTrue("file path is empty " + file_swa, !(fm.getFilePath() == null) && !fm.getFilePath().isEmpty()); // FindAllTheFiles doesn't actually populate this information, go figure Assert.assertTrue("file md5sum is wrong for " + file_swa, fm.getMd5sum().equals(Integer.toString(file_swa + 42))); Assert.assertTrue("file size is wrong ", fm.getSize().equals((long) file_swa + 1701)); Assert.assertTrue("file description is empty " + file_swa, !(fm.getDescription() == null) && !fm.getDescription().isEmpty()); Assert.assertTrue("meta type is empty" + file_swa, !(fm.getMetaType() == null) && !fm.getMetaType().isEmpty()); return false; } } public class TestingDecider extends BasicDecider { private final Set<String> fileSet = new HashSet<>(); private int finalChecks = 0; private int launches = 0; public int getLaunches() { return launches; } public int getFileCount() { return fileSet.size(); } public int getFinalChecks() { return finalChecks; } @Override protected boolean reportLaunch() { launches = launches + 1; return false; } @Override protected ReturnValue doFinalCheck(String commaSeparatedFilePaths, String commaSeparatedParentAccessions) { ReturnValue returnValue = super.doFinalCheck(commaSeparatedFilePaths, commaSeparatedParentAccessions); finalChecks = finalChecks + 1; return returnValue; } @Override public ReturnValue init() { Log.debug("INIT"); fileSet.clear(); // reset count finalChecks = 0; launches = 0; //this.setHeader(Header.IUS_SWA); //this.setMetaType(Arrays.asList("application/bam")); //allows anything defined on the command line to override the 'defaults' here. ReturnValue val = super.init(); return val; } @Override protected String handleGroupByAttribute(String attribute) { fileSet.add(attribute); Log.debug("GROUP BY ATTRIBUTE: " + getHeader().getTitle() + " " + attribute); return attribute; } @Override protected boolean checkFileDetails(ReturnValue returnValue, FileMetadata fm) { Log.debug("CHECK FILE DETAILS:" + fm); //pathToAttributes.put(fm.getFilePath(), returnValue); return super.checkFileDetails(returnValue, fm); } @Override protected Map<String, String> modifyIniFile(String commaSeparatedFilePaths, String commaSeparatedParentAccessions) { Log.debug("INI FILE:" + commaSeparatedFilePaths); Map<String, String> iniFileMap = new TreeMap<>(); iniFileMap.put(ReservedIniKeys.INPUT_FILE.getKey(), commaSeparatedFilePaths); return iniFileMap; } } @Test public void testIsContained_Same() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R2_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance) .isToRunContained(metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun)); } @Test public void testIsContained_SameSize_different_set() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://non_matching_file"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(!((BasicDecider) instance) .isToRunContained(metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun)); } @Test public void testIsContained_More() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R2_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R3_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(!((BasicDecider) instance) .isToRunContained(metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun)); } @Test public void testIsContained_Less() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance) .isToRunContained(metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun)); } /** * <p>testCompareWorkflowRunFiles_Same.</p> */ @Test public void testCompareWorkflowRunFiles_Same() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R2_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles( metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun) == BasicDecider.FILE_STATUS.SAME_FILES); } /** * <p>testCompareWorkflowRunFiles_Same.</p> */ @Test public void testCompareWorkflowRunFiles_BothEmpty() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); List<String> filesToRun = new ArrayList<>(); //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles(new HashSet<Integer>(), filesToRun) == BasicDecider.FILE_STATUS.SAME_FILES); } /** * <p>testCompareWorkflowRunFiles_Bigger.</p> */ @Test public void testCompareWorkflowRunFiles_Bigger() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R2_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R3_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles( metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun) == BasicDecider.FILE_STATUS.PAST_SUBSET_OR_INTERSECTION); } /** * <p>testCompareWorkflowRunFiles_SameButDifferent.</p> */ @Test public void testCompareWorkflowRunFiles_SameButDifferent() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); filesToRun.add("s3://abcco.uploads/s_G1_L001_R3_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles( metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun) == BasicDecider.FILE_STATUS.PAST_SUBSET_OR_INTERSECTION); } /** * <p>testCompareWorkflowRunFiles_Smaller.</p> */ @Test public void testCompareWorkflowRunFiles_Smaller() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://abcco.uploads/s_G1_L001_R1_001_index8.fastq.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Set<Integer> inputFiles = metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles(inputFiles, filesToRun) == BasicDecider.FILE_STATUS.PAST_SUPERSET); } /** * <p>testCompareWorkflowRunFiles_Smaller.</p> */ @Test public void testCompareWorkflowRunFiles_Disjoint() { TestingDecider decider = (TestingDecider) instance; decider.setMetaws((MetadataWS) metadata); decider.setMetaType(fastq_gz); List<String> filesToRun = new ArrayList<>(); filesToRun.add("s3://garbage.gz"); int workflowRunAcc = 6654; //assertTrue(result.getStdout().contains("UNIT_TEST_TOKEN")); Assert.assertTrue(((BasicDecider) instance).compareWorkflowRunFiles( metadata.getWorkflowRun(workflowRunAcc).getInputFileAccessions(), filesToRun) == BasicDecider.FILE_STATUS.DISJOINT_SETS); } /** * Don't use the output of this thing unless you really really have to * stdout can change a lot * @param params * @return */ protected String launchAndCaptureOutput(String[] params) { ByteArrayOutputStream testOut = new ByteArrayOutputStream(); System.setOut(new PrintStream(testOut)); launchPlugin(params); String redirected = testOut.toString(); System.setOut(System.out); return redirected; } }