/**
* {@inheritDoc}
*
* @return
*/
@Override
public ReturnValue clean_up() {
try {
writer.flush();
writer.close();
if (options.has("stdout")) {
Log.stdout(writer.toString());
}
} catch (IOException ex) {
Log.error("Writer is already closed.", ex);
}
return ret;
}
/**
* getHtml.
*
* @param obj a {@link java.lang.Object} object.
* @param registration a {@link net.sourceforge.seqware.common.model.Registration} object.
* @param listSeqencerRunNodeId a {@link java.util.List} object.
* @param treeType a {@link java.lang.String} object.
* @return a {@link java.lang.String} object.
*/
public static String getHtml(
Object obj, Registration registration, List<String> listSeqencerRunNodeId, String treeType) {
String html = "";
if (obj instanceof SequencerRun) {
html = getAllHtml((SequencerRun) obj, registration, null, treeType);
}
if (obj instanceof Lane) {
html = getAllHtml((Lane) obj, registration, null, treeType);
}
if (obj instanceof IUS) {
Log.info("ius call");
html = getAllHtml((IUS) obj, registration, null, false, false, treeType);
}
if (obj instanceof Processing) {
html =
getAllHtml(
(Processing) obj,
registration,
null,
0,
listSeqencerRunNodeId,
true,
false,
treeType);
}
return html;
}
/** getXml. */
@Get
public void getXml() {
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Lane dto;
authenticate();
LaneService ss = BeanFactory.getLaneServiceBean();
Lane lane = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Lane>[] createCollectionPropertyNames =
CollectionPropertyName.createCollectionPropertyNames(
Lane.class, new String[] {"laneAttributes"});
dto =
copier.hibernate2dto(
Lane.class,
lane,
new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
createCollectionPropertyNames);
if (fields.contains("sequencerRun")) {
SequencerRun sr = lane.getSequencerRun();
if (sr != null) {
SequencerRun copySR = copier.hibernate2dto(SequencerRun.class, sr);
dto.setSequencerRun(copySR);
} else {
Log.info("Could not be found sequencer run");
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
private void reportWorkflowRunStdErrOut(String workflowRunAccession, int streamType)
throws IOException {
String title = "workflowrun_" + workflowRunAccession;
if (streamType == 1) {
title = title + "_STDOUT";
initWriter(title);
writer.write(metadata.getWorkflowRunReportStdOut(Integer.parseInt(workflowRunAccession)));
} else if (streamType == 2) {
title = title + "_STDERR";
initWriter(title);
writer.write(metadata.getWorkflowRunReportStdErr(Integer.parseInt(workflowRunAccession)));
} else {
Log.error(
"Unknown stream type: "
+ streamType
+ " should be "
+ WorkflowRunReporter.STDERR
+ " for stderr or "
+ WorkflowRunReporter.STDOUT
+ " for stdout!");
initWriter(title);
writer.write(
"Unknown stream type: "
+ streamType
+ " should be "
+ WorkflowRunReporter.STDERR
+ " for stderr or "
+ WorkflowRunReporter.STDOUT
+ " for stdout!");
}
}
private void reportOnWorkflow(
String workflowAccession, WorkflowRunStatus status, Date earlyDate, Date lateDate)
throws IOException {
String title = "";
if (workflowAccession != null) {
title = "workflow_" + workflowAccession;
}
if (status != null) {
title += "status_" + status.name();
}
if (earlyDate != null) {
title += "from" + dateFormat.format(earlyDate);
}
if (lateDate != null) {
title += "to" + dateFormat.format(lateDate);
}
initWriter(title);
String report;
try {
Integer workflowParameter = null;
if (workflowAccession != null) {
workflowParameter = Integer.parseInt(workflowAccession);
}
report = metadata.getWorkflowRunReport(workflowParameter, status, earlyDate, lateDate);
} catch (RuntimeException e) {
Log.fatal("Workflow not found", e);
ret = new ReturnValue(ReturnValue.INVALIDPARAMETERS);
return;
}
if (options.has("human")) {
writer.write(TabExpansionUtil.expansion(report));
return;
}
writer.write(report);
}
/** getXml. */
@Get
public void getXml() {
authenticate();
WorkflowService ss = BeanFactory.getWorkflowServiceBean();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
JaxbObject<Workflow> jaxbTool = new JaxbObject<Workflow>();
Workflow workflow = (Workflow) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
Workflow dto = copier.hibernate2dto(Workflow.class, workflow);
if (fields.contains("params")) {
SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
if (wps != null) {
SortedSet<WorkflowParam> copiedParams = new TreeSet<WorkflowParam>();
for (WorkflowParam param : workflow.getWorkflowParams()) {
copiedParams.add(copier.hibernate2dto(WorkflowParam.class, param));
}
dto.setWorkflowParams(copiedParams);
} else {
Log.info("Could not be found: workflow params");
}
}
if (fields.contains("attributes")) {
Set<WorkflowAttribute> was = workflow.getWorkflowAttributes();
if (was != null && !was.isEmpty()) {
Set<WorkflowAttribute> newwas = new TreeSet<WorkflowAttribute>();
for (WorkflowAttribute wa : was) {
newwas.add(copier.hibernate2dto(WorkflowAttribute.class, wa));
}
dto.setWorkflowAttributes(newwas);
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
@Test
public void testMonitoring() throws IOException {
String listCommand =
"-p net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker -- --tp 1000";
String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS);
Log.info(listOutput);
}
@Test
public void testLaunchScheduled() throws IOException {
// launch-scheduled
String schedCommand =
"-p net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher -- --launch-scheduled";
String schedOutput = ITUtility.runSeqWareJar(schedCommand, ReturnValue.SUCCESS);
Log.info(schedOutput);
}
/** close. */
public static synchronized void close() {
if (metadataDBWrapper.get() != null) {
Log.debug(metadataDBWrapper.get().toString() + " was closed ");
metadataDBWrapper.get().clean_up();
metadataDBWrapper.set(null);
// db = null;
}
}
private String getNameNode(Integer id, String typeNode) {
String name = "";
if ("st".equals(typeNode)) {
Log.info("find Study");
name = getStudyService().findByID(id).getTitle();
}
if ("exp".equals(typeNode)) {
Log.info("find Experiment");
name = getExperimentService().findByID(id).getTitle();
}
if ("sam".equals(typeNode)) {
Log.info("find Sample");
name = getSampleService().findByID(id).getTitle();
}
if ("seq".equals(typeNode)) {
Log.info("find Lane");
name = getLaneService().findByID(id).getName();
}
if ("ius".equals(typeNode)) {
Log.info("find IUS");
name = getIUSService().findByID(id).getName();
}
if ("ae".equals(typeNode)) {
Log.info("find Study");
name = "SWID " + getProcessingService().findByID(id).getSwAccession().toString();
}
if ("sr".equals(typeNode)) {
Log.info("find Seq Run");
name = getSequencerRunService().findByID(id).getName();
}
return name;
}
/** getXml. */
@Get
public void getXml() {
authenticate();
JaxbObject<Lane> jaxbTool = new JaxbObject<>();
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
SampleService ss = BeanFactory.getSampleServiceBean();
Sample sample = testIfNull(ss.findBySWAccession(getId()));
CollectionPropertyName<Sample>[] createCollectionPropertyNames =
CollectionPropertyName.createCollectionPropertyNames(
Sample.class, new String[] {"sampleAttributes"});
Sample dto =
copier.hibernate2dto(
Sample.class, sample, new Class<?>[] {}, createCollectionPropertyNames);
if (fields.contains("lanes")) {
SortedSet<Lane> lanes = sample.getLanes();
if (lanes != null) {
SortedSet<Lane> copiedLanes = new TreeSet<>();
for (Lane lane : lanes) {
copiedLanes.add(copier.hibernate2dto(Lane.class, lane));
}
dto.setLanes(copiedLanes);
} else {
Log.info("Could not be found: lanes");
}
}
if (fields.contains("ius")) {
SortedSet<IUS> ius = sample.getIUS();
if (ius != null) {
SortedSet<IUS> copiedIUS = new TreeSet<>();
for (IUS i : ius) {
copiedIUS.add(copier.hibernate2dto(IUS.class, i));
}
dto.setIUS(copiedIUS);
}
{
Log.info("Could not be found : ius");
}
}
Document line = XmlTools.marshalToDocument(jaxbTool, dto);
getResponse().setEntity(XmlTools.getRepresentation(line));
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public String get_syntax() {
try {
parser.printHelpOn(System.err);
} catch (IOException e) {
// TODO Auto-generated catch block
Log.fatal(e);
}
return ("");
}
/**
* getInstance.
*
* @return a {@link net.sourceforge.seqware.common.ContextImpl} object.
*/
public static synchronized ContextImpl getInstance() {
if (ctx == null) {
ApplicationContext c = ContextLoader.getCurrentWebApplicationContext();
if (c == null) {
Log.info("ContextImpl: Could not find web context. Switching to XML context.");
c = new ClassPathXmlApplicationContext("applicationContext.xml");
}
ctx = (ContextImpl) c.getBean("contextImpl");
}
return ctx;
}
/**
* Given a workflowRunAcc returns a list of file paths that were used in that run using
* effectively, the workflow run reporter.
*
* <p>Hopefully, this is the last we'll use this approach!
*
* @param workflowRunAcc
* @param filesToRun
* @return
*/
private List<Integer> getListOfFiles(int workflowRunAcc) {
Map<String, String> map = generateWorkflowRunMap(workflowRunAcc);
List<Integer> ranOnList = new ArrayList<>();
if (map.isEmpty()) {
return ranOnList;
}
String ranOnString = map.get("Immediate Input File SWIDs");
if (ranOnString == null) {
return ranOnList;
}
String[] ranOnArr = ranOnString.split(",");
if (ranOnString.isEmpty()) {
return ranOnList;
}
for (String i : ranOnArr) {
ranOnList.add(Integer.valueOf(i.trim()));
Log.trace("Adding item: " + i);
}
Log.debug("Got list of files: " + StringUtils.join(ranOnList, ','));
return ranOnList;
}
@Test
public void runDatabaseCheck() throws IOException {
String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB";
String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, null);
Log.info(listOutput);
String[] split = listOutput.split("Printed report to ");
File report = new File(split[split.length - 1].trim());
String readFileToString = FileUtils.readFileToString(report, (Charset) null);
Assert.assertTrue("report empty", readFileToString.length() > 0);
Assert.assertTrue(
"report does not contain report", readFileToString.contains("CheckDB Report"));
Assert.assertTrue("report contains exceptions", !readFileToString.contains("Exception"));
FileUtils.deleteQuietly(report);
}
/**
* get.
*
* @return a {@link net.sourceforge.seqware.common.metadata.MetadataDB} object.
*/
public static synchronized MetadataDB get() {
try {
if (metadataDBWrapper.get() != null
&& ((metadataDBWrapper.get().getDb() != null
&& metadataDBWrapper.get().getDb().isClosed())))
// || db.getSql()!=null && db.getSql().isClosed()))
{
metadataDBWrapper.get().clean_up();
metadataDBWrapper.set(null);
// db = null;
}
} catch (SQLException ex) {
Log.error("Closing DB connection and creating a new one failed", ex);
}
if (metadataDBWrapper.get() == null) {
metadataDBWrapper.set(new MetadataDB());
// Log.debug("DBAccess is using " + user + " " + pass + " on " + connection);
DataSource ds = null;
try {
InitialContext initCtx = new InitialContext();
ds = (DataSource) initCtx.lookup("java:comp/env/jdbc/SeqWareMetaDB");
} catch (NamingException ex) {
Log.fatal(ex);
ex.printStackTrace();
}
if (ds != null) {
Log.debug("init via db.init(ds), datasource is " + ds.getClass());
metadataDBWrapper.get().init(ds);
} else {
Log.debug("init via init(user,pass,connection)");
Map<String, String> settings = null;
try {
settings = ConfigTools.getSettings();
String connection =
"jdbc:postgresql://" + settings.get("SW_DB_SERVER") + "/" + settings.get("SW_DB");
String user = settings.get("SW_DB_USER");
String pass = settings.get("SW_DB_PASS");
Log.debug("DBAccess is using " + user + " " + pass + " on " + connection);
metadataDBWrapper.get().init(connection, user, pass);
} catch (Exception ex) {
Log.fatal("get() could not init ", ex);
Logger.getLogger(DBAccess.class.getName()).log(Level.SEVERE, null, ex);
}
}
}
Log.debug(metadataDBWrapper.get().toString() + " was returned ");
return metadataDBWrapper.get();
}
/** {@inheritDoc} */
@Override
@Put
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Experiment newObj = null;
JaxbObject<Experiment> jo = new JaxbObject<Experiment>();
try {
String text = entity.getText();
newObj = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text);
} catch (SAXException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e);
}
try {
ExperimentService service = BeanFactory.getExperimentServiceBean();
Experiment exp = (Experiment) testIfNull(service.findByID(newObj.getExperimentId()));
exp.givesPermission(registration);
// simple types
String title = newObj.getTitle();
String name = newObj.getName();
String desc = newObj.getDescription();
String alias = newObj.getAlias();
String accession = newObj.getAccession();
String status = newObj.getStatus();
String centerName = newObj.getCenterName();
String sequencerSpace = newObj.getSequenceSpace();
String baseCaller = newObj.getBaseCaller();
String qualityScorer = newObj.getQualityScorer();
Integer qualityNumberLevels = newObj.getQualityNumberOfLevels();
Integer qualityMultiplier = newObj.getQualityMultiplier();
Long expectedNumberSpots = newObj.getExpectedNumberSpots();
Long expectedNumberReads = newObj.getExpectedNumberReads();
// foreign keys
Study study = newObj.getStudy();
Registration owner = newObj.getOwner();
// sets
Set<ExperimentAttribute> expAttributes = newObj.getExperimentAttributes();
if (title != null) {
exp.setTitle(title);
}
if (name != null) {
exp.setName(name);
}
if (desc != null) {
exp.setDescription(desc);
}
if (alias != null) {
exp.setAlias(alias);
}
if (accession != null) {
exp.setAccession(accession);
}
if (status != null) {
exp.setStatus(status);
}
if (centerName != null) {
exp.setCenterName(centerName);
}
if (sequencerSpace != null) {
exp.setSequenceSpace(sequencerSpace);
}
if (baseCaller != null) {
exp.setBaseCaller(baseCaller);
}
if (qualityScorer != null) {
exp.setQualityScorer(qualityScorer);
}
if (qualityNumberLevels != null) {
exp.setQualityNumberOfLevels(qualityNumberLevels);
}
if (qualityMultiplier != null) {
exp.setQualityMultiplier(qualityMultiplier);
}
if (expectedNumberSpots != null) {
exp.setExpectedNumberSpots(expectedNumberSpots);
}
if (expectedNumberReads != null) {
exp.setExpectedNumberReads(expectedNumberReads);
}
if (study != null) {
StudyService ss = BeanFactory.getStudyServiceBean();
Study newStudy = ss.findByID(study.getStudyId());
if (newStudy != null && newStudy.givesPermission(registration)) {
exp.setStudy(newStudy);
} else if (newStudy == null) {
Log.info("Could not be found " + study);
}
}
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
exp.setOwner(newReg);
} else {
Log.info("Could not be found " + owner);
}
} else if (exp.getOwner() == null) {
exp.setOwner(registration);
}
if (null != expAttributes) {
exp.getExperimentAttributes().clear();
for (ExperimentAttribute ea : expAttributes) {
ea.setExperiment(exp);
exp.getExperimentAttributes().add(ea);
}
}
service.update(registration, exp);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Experiment detachedLane = copier.hibernate2dto(Experiment.class, exp);
Document line = XmlTools.marshalToDocument(jo, detachedLane);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(
getRequest().getRootRef() + "/experiments/" + detachedLane.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
return representation;
}
/** {@inheritDoc} */
@Override
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Workflow newWorkflow = null;
JaxbObject<Workflow> jo = new JaxbObject<Workflow>();
try {
String text = entity.getText();
newWorkflow = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
} catch (SAXException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex.getMessage());
} catch (IOException e) {
e.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
}
try {
WorkflowService fs = BeanFactory.getWorkflowServiceBean();
Workflow workflow = (Workflow) testIfNull(fs.findByID(newWorkflow.getWorkflowId()));
workflow.givesPermission(registration);
// simple types
String name = newWorkflow.getName();
String desc = newWorkflow.getDescription();
String baseIniFile = newWorkflow.getBaseIniFile();
String command = newWorkflow.getCommand();
String cwd = newWorkflow.getCwd();
String host = newWorkflow.getHost();
String inputAlgorithm = newWorkflow.getInputAlgorithm();
String permanentBundleLocation = newWorkflow.getPermanentBundleLocation();
String seqwareVersion = newWorkflow.getSeqwareVersion();
String template = newWorkflow.getTemplate();
String username = newWorkflow.getUsername();
String version = newWorkflow.getVersion();
// foreign keys
Registration owner = newWorkflow.getOwner();
workflow.setName(name);
workflow.setDescription(desc);
workflow.setBaseIniFile(baseIniFile);
workflow.setCommand(command);
workflow.setCwd(cwd);
workflow.setHost(host);
workflow.setInputAlgorithm(inputAlgorithm);
workflow.setPermanentBundleLocation(permanentBundleLocation);
workflow.setSeqwareVersion(seqwareVersion);
workflow.setTemplate(template);
workflow.setUsername(username);
workflow.setVersion(version);
workflow.setUpdateTimestamp(new Date());
workflow.setWorkflowClass(newWorkflow.getWorkflowClass());
workflow.setWorkflowType(newWorkflow.getWorkflowType());
workflow.setWorkflowEngine(newWorkflow.getWorkflowEngine());
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
workflow.setOwner(newReg);
} else {
Log.info("Could not be found: " + owner);
}
} else if (workflow.getOwner() == null) {
workflow.setOwner(registration);
}
if (newWorkflow.getWorkflowAttributes() != null) {
workflow.getWorkflowAttributes().clear();
for (WorkflowAttribute wfa : newWorkflow.getWorkflowAttributes()) {
wfa.setWorkflow(workflow);
workflow.getWorkflowAttributes().add(wfa);
}
}
fs.update(registration, workflow);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Workflow detachedWorkflow = copier.hibernate2dto(Workflow.class, workflow);
Document line = XmlTools.marshalToDocument(jo, detachedWorkflow);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(
getRequest().getRootRef() + "/workflows/" + detachedWorkflow.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
return representation;
}
/** {@inheritDoc} */
@Override
public ReturnValue do_run() {
ReturnValue ret = new ReturnValue();
ret.setRunStartTstmp(new Date());
// Append initial command and options
StringBuffer cmd = new StringBuffer(srf2FastqPath);
cmd.append(" -c ");
// filter bad reads if requested
if (filter) {
cmd.append(" -C ");
}
// If multiple ends, they should be sequential if bfast
if (ends > 1 && "bfast".equals(aligner)) {
cmd.append(" -S ");
}
// for bwa should be two different files, give the base as the first outputFile
// NOTE: this means BWA output is one or two files, there's not shreading implemented for large
// inputs
else if (ends > 1 && "bwa".equals(aligner)) {
cmd.append(" -n -s " + outputFiles.get(0) + " ");
}
// For paired end Illumina runs, add options to reverse compliments ends
// great than 1
/* Brian 20101215: I don't think this is actually needed
if (ends > 1 && sequencer.compareTo("illumina-ga2") == 0) {
cmd.append(" -r 1");
for (int i = 2; i < ends; i++)
cmd.append("," + i);
cmd.append(" ");
}*/
// For Solid, have to add option to append Primer to Sequence
if (sequencer.indexOf("AB_SOLiD_") > -1) {
cmd.append(" -e ");
}
// Add file name to the end
cmd.append(" " + input);
// Run command
Process p = null;
Log.error("Starting srf2fastq"); // FIXME
try {
Log.error("Executing: " + cmd.toString());
p = Runtime.getRuntime().exec(cmd.toString());
} catch (IOException e) {
return new ReturnValue(null, e.toString(), 4);
}
Log.error("srf2fastq launched"); // FIXME
// we're only parsing stdout and managing file creation for BFAST output (all one file)
if ("bfast".equals(aligner) || ("bwa".equals(aligner) && ends == 1)) {
// Read from stdout and write to output files. Each output file gets 4 *
// ends before moving to next entry. This assures all ends for a given
// read are together
try {
// FIXME: This first function call is just for now, srf2fastq strips
// primer automatically
if (sequencer.indexOf("AB_SOLiD_") > -1) {
StdOut.stdout2fileEncodedStripQualPrimer(p, outputFiles, ends * 4);
} else {
StdOut.stdout2file(p, outputFiles, false, ends * 4);
}
} catch (IOException e) {
// FIXME: Need to clean up error codes and all
p.destroy();
return new ReturnValue(null, "stdout2file encountered an error", 4);
}
}
// else we let srf2fastq make the files for us
else if ("bwa".equals(aligner) && ends > 1) {
// the command will just run as prepared, don't need to process stdout
}
// Wait on process
try {
p.waitFor();
} catch (InterruptedException e) {
p.destroy();
return new ReturnValue(null, e.toString(), 4);
}
Log.error("srf2fastq done"); // FIXME
// Otherwise return exit code
ret.setExitStatus(p.exitValue());
try {
ret.setStderr(StdErr.stderr2string(p));
ret.setExitStatus(p.exitValue());
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
ret.setRunStopTstmp(new Date());
return ret;
}
/** {@inheritDoc} */
@Override
public ReturnValue init() {
ReturnValue ret = new ReturnValue();
// some basics
ret.setAlgorithm("SRF2Fastq");
ret.setDescription(
"This module converts an SRF file to a Fastq for use with aligners. The output is Sanger scaled.");
ret.setVersion("0.7.1");
// Parse relevant parameters
for (int i = 0; i < this.getParameters().size(); i++) {
if (this.getParameters().get(i).compareTo("-a") == 0
|| this.getParameters().get(i).compareTo("--aligner") == 0) {
aligner = this.getParameters().get(++i).toLowerCase();
} else if (this.getParameters().get(i).compareTo("-s") == 0
|| this.getParameters().get(i).compareTo("--sequencer") == 0) {
sequencer = this.getParameters().get(++i).toLowerCase();
} else if (this.getParameters().get(i).compareTo("-b") == 0
|| this.getParameters().get(i).compareTo("--bin") == 0) {
srf2FastqPath = this.getParameters().get(++i);
} else if (this.getParameters().get(i).compareTo("-f") == 0
|| this.getParameters().get(i).compareTo("--filter") == 0) {
filter = true;
} else if (this.getParameters().get(i).compareTo("-e") == 0
|| this.getParameters().get(i).compareTo("--ends") == 0) {
try {
ends = Integer.parseInt(this.getParameters().get(++i));
} catch (NumberFormatException e) {
ends = 0;
}
} else if (this.getParameters().get(i).compareTo("-i") == 0
|| this.getParameters().get(i).compareTo("--input") == 0) {
input = this.getParameters().get(++i);
} else if (this.getParameters().get(i).compareTo("-n") == 0
|| this.getParameters().get(i).compareTo("--num-output-files") == 0) {
try {
numOut = Integer.parseInt(this.getParameters().get(++i));
} catch (NumberFormatException e) {
numOut = 1;
}
} else if (this.getParameters().get(i).compareTo("-o") == 0
|| this.getParameters().get(i).compareTo("--output-prefix") == 0) {
outputPrefix = this.getParameters().get(++i);
}
}
// Set prefix if not defined
if (outputPrefix == null) {
// Strip off directories before
Log.error("INPUT: " + input);
int start = input.lastIndexOf(System.getProperty("file.separator"));
if (start < 0) start = 0;
// Strip off .srf ending
int end = input.lastIndexOf(".srf");
if (end > 0) outputPrefix = input.substring(start + 1, end);
}
// for bwa output only make 1 output file (single end) or 2 output files (paired end)
if ("bwa".equals(aligner)) {
File file = new File(outputPrefix);
if (file.getParentFile() != null) file.getParentFile().mkdirs();
if (ends > 1) {
outputFiles.add(file);
} else {
String outputFileName = new String(outputPrefix + ".fastq");
file = new File(outputFileName);
outputFiles.add(file);
}
} else if ("bfast".equals(aligner)) {
// Setup output files for BFAST, supports multiple output files for large inputs
for (int i = 0; i < numOut; i++) {
String outputFileName = new String(outputPrefix + "." + i + ".fastq");
File file = new File(outputFileName);
// Make directory if needed
if (file.getParentFile() != null) file.getParentFile().mkdirs();
// Make sure we can write to this file
try {
file.createNewFile();
} catch (IOException e) {
// FIXME: If file exists, continue anyway. Should we do this?
}
if (!file.canWrite()) {
ret.setStderr("File " + outputFileName + " could not be created in a writable manner\n");
ret.setExitStatus(ReturnValue.FILENOTWRITABLE);
return ret;
}
// Otherwise we are in the clear, so add to file array
outputFiles.add(file);
}
}
// If we got here, no problems, so we are good
ret.setExitStatus(ReturnValue.SUCCESS);
return ret;
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public ReturnValue do_run() {
try {
String timePeriod = null;
WorkflowRunStatus status = options.valueOf(statusSpec);
if (options.has("time-period")) {
timePeriod = (String) options.valueOf("time-period");
}
/*
* FIXME: I think this is problematic since the DB may use GMT whereas the Date() command returns something localized (I think).
* We need to standardize on date/time across out DB and Java code.
*/
Date firstDate = null, lastDate = null;
if (timePeriod != null) {
String[] dates = timePeriod.trim().split(":");
SimpleDateFormat localDateFormat = new SimpleDateFormat("yyyy-MM-dd");
try {
firstDate = localDateFormat.parse(dates[0].trim());
if (dates.length != 1) {
lastDate = localDateFormat.parse(dates[1].trim());
}
} catch (ParseException ex) {
Log.warn(
"Date not found. Date must be in format YYYY-MM-DD or YYYY-MM-DD:YYYY-MM-DD.", ex);
println("Incorrect date");
ret = new ReturnValue(ReturnValue.INVALIDPARAMETERS);
return ret;
}
if (lastDate == null) {
lastDate = new Date();
}
}
if (options.has(WRSTDERR) && options.has(WRSTDOUT)) {
println("Combination of both stdout and stderr not recognized");
ret.setExitStatus(ReturnValue.INVALIDPARAMETERS);
return ret;
}
if (options.has("workflow-run-accession")) {
String wra = (String) options.valueOf("workflow-run-accession");
if (options.has(WRSTDERR)) {
reportWorkflowRunStdErrOut(wra, STDERR);
} else if (options.has(WRSTDOUT)) {
reportWorkflowRunStdErrOut(wra, STDOUT);
} else {
reportOnWorkflowRun(wra);
}
} else if (options.has("workflow-accession") || options.has(statusSpec)) {
String tp = (String) options.valueOf("workflow-accession");
reportOnWorkflow(tp, status, firstDate, lastDate);
}
/**
* SEQWARE-863 ability to query without specifying a specific workflow-accession was removed
* else if (firstDate != null || lastDate != null) { reportOnWorkflowRuns(firstDate,
* lastDate);
*/
else {
println("Combination of parameters not recognized!");
println(this.get_syntax());
ret.setExitStatus(ReturnValue.INVALIDPARAMETERS);
return ret;
}
} catch (IOException e) {
Log.error(e.getMessage(), e);
ret.setExitStatus(ReturnValue.FILENOTREADABLE);
ret.setDescription(e.getMessage());
}
return ret;
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
public ReturnValue do_run() {
ReturnValue ret = new ReturnValue();
ResultSet rs = null;
MetadataDB mdb = null;
PreparedStatement prepareStatement = null;
try {
String query =
new StringBuilder()
.append(
"select w.sw_accession, w.workflow_run_id, w.status, f.* FROM workflow_run w LEFT OUTER JOIN workflow_run_input_files f ")
.append(
"ON w.workflow_run_id = f.workflow_run_id WHERE (status = 'completed' OR status= 'failed') AND ")
.append("f.workflow_run_id IS NULL ORDER BY w.sw_accession;")
.toString();
Log.info("Executing query: " + query);
mdb = DBAccess.get();
List<int[]> ids =
mdb.executeQuery(
query,
new ResultSetHandler<List<int[]>>() {
@Override
public List<int[]> handle(ResultSet rs) throws SQLException {
List<int[]> ids = new ArrayList<>();
while (rs.next()) {
ids.add(new int[] {rs.getInt("sw_accession"), rs.getInt("workflow_run_id")});
}
return ids;
}
});
mdb.getDb().setAutoCommit(false);
prepareStatement =
mdb.getDb()
.prepareStatement(
"INSERT INTO workflow_run_input_files (workflow_run_id, file_id) VALUES(?,?)");
for (int[] i : ids) {
int workflowSWID = i[0];
int workflowRunID = i[1];
Log.stdout("Working on workflow_run " + workflowSWID);
// populate input files
List<Integer> listOfFiles = this.getListOfFiles(workflowSWID);
Log.stdout("Found " + listOfFiles.size() + " input files for workflow_run " + workflowSWID);
// insert into new workflow_run_input_files table
for (Integer fSWID : listOfFiles) {
Integer fileID = this.metadata.getFile(fSWID).getFileId();
prepareStatement.setInt(1, workflowRunID);
prepareStatement.setInt(2, fileID);
prepareStatement.executeUpdate();
}
}
Log.stdout("Success!");
mdb.getDb().commit();
return ret;
} catch (SQLException ex) {
Log.fatal("Population failed, aborting.");
Logger.getLogger(WorkflowRunFilesInitialPopulationPlugin.class.getName())
.log(Level.SEVERE, null, ex);
ret.setExitStatus(ReturnValue.FAILURE);
} finally {
if (mdb != null) {
DbUtils.closeQuietly(mdb.getDb(), mdb.getSql(), rs);
}
DBAccess.close();
DbUtils.closeQuietly(prepareStatement);
}
ret.setExitStatus(ReturnValue.FAILURE);
return ret;
}
/**
* getAllHtml.
*
* @param processing a {@link net.sourceforge.seqware.common.model.Processing} object.
* @param registration a {@link net.sourceforge.seqware.common.model.Registration} object.
* @param openingNodeId a {@link java.lang.String} object.
* @param currPosId a {@link java.lang.Integer} object.
* @param listNodeId a {@link java.util.List} object.
* @param isFirstCall a boolean.
* @param isViewCurrentNode a boolean.
* @param treeType a {@link java.lang.String} object.
* @return a {@link java.lang.String} object.
*/
public static String getAllHtml(
Processing processing,
Registration registration,
String openingNodeId,
Integer currPosId,
List<String> listNodeId,
boolean isFirstCall,
boolean isViewCurrentNode,
String treeType) {
currPosId++;
String id = getParentId(currPosId, listNodeId);
if (id.indexOf("wfr_") != -1) {
currPosId++;
id = getParentId(currPosId, listNodeId);
}
if (id.indexOf("sr_") != -1 && !isViewCurrentNode) {
SequencerRun sequencerRun = getParentSequencerRun(processing, Constant.getId(id));
if (sequencerRun == null) {
return "";
}
Log.info("openingNodeId = " + openingNodeId);
return getAllHtml(
sequencerRun, registration, openingNodeId /*processing.getProcessingId()*/, treeType);
} else if (id.indexOf("seq_") != -1 && !isViewCurrentNode) {
Lane lane = getParentLane(processing, Constant.getId(id));
if (lane == null) {
return "";
}
return getAllHtml(lane, registration, openingNodeId, treeType);
// 1 return getAllHtml(lane, registration, processing.getProcessingId());
// 2 return getAllHtml(lane, registration, processing.getProcessingId(), isOpenProc, true);
} else if (id.indexOf("ius_") != -1 && !isViewCurrentNode) {
Log.info("Proc IUS HTML");
IUS ius = getParentIUS(processing, Constant.getId(id));
if (ius == null) {
return "";
}
return getAllHtml(ius, registration, openingNodeId, !isFirstCall, true, treeType);
} else {
Processing currProc;
if (isFirstCall) {
currProc = processing;
} else {
currProc = getParentProcessing(processing, Constant.getId(id));
if (currProc == null) {
return "";
}
openingNodeId = getParentId(currPosId - 1, listNodeId);
if (openingNodeId.indexOf("wfr_") != -1) {
openingNodeId = getParentId(currPosId - 2, listNodeId);
}
}
Log.info(" -> openingNodeId Proc = " + openingNodeId);
String childHtml =
NodeHtmlUtil.getProcessingHtml(
currProc, registration, TYPE_TREE, openingNodeId, treeType);
String parentHtml =
getAllHtml(currProc, registration, id, currPosId, listNodeId, false, false, treeType);
String parentId = Constant.PROCESSING_PREFIX + currProc.getProcessingId();
return NodeHtmlUtil.pasteHtmlIntoParentNode(childHtml, parentHtml, parentId, true);
// Log.info("currProcId = " + currProc.getProcessingId());
// String childHtml = NodeHtmlUtil.getProcessingHtml(currProc, registration, TYPE_TREE,
// openingNodeId);
// String parentHtml = getAllHtml(currProc, registration, currProc.getProcessingId(),
// currPosId, listNodeId, false, false);
// String parentId = Constant.PROCESSING_PREFIX + currProc.getProcessingId();
// return NodeHtmlUtil.pasteHtmlIntoParentNode(childHtml, parentHtml, parentId, true);
}
}
/**
* Handles the user's request to submit a new study.
*
* @param request HttpServletRequest
* @param response HttpServletResponse
* @param command Study command object
* @return ModelAndView
* @throws java.lang.Exception if any.
*/
public ModelAndView handleSubmit(
HttpServletRequest request, HttpServletResponse response, UploadFile command)
throws Exception {
Registration registration = Security.getRegistration(request);
if (registration == null) return new ModelAndView("redirect:/login.htm");
ServletContext context = this.getServletContext();
command.setFolderStore(context.getInitParameter("path.to.upload.directory"));
command.setStrStartURL(context.getInitParameter("true.protocols"));
ModelAndView modelAndView = null;
BindingResult errors = this.validate(request, command);
if (errors.hasErrors()) {
Map model = errors.getModel();
Integer id = getRequestedId(request);
String typeNode = getRequestedTypeNode(request);
String nameNode = getNameNode(id, typeNode);
List<FileType> listFileType = getFileTypeService().list();
model.put("id", id);
model.put("tn", typeNode);
model.put("nameNode", nameNode);
model.put("listFileType", listFileType);
modelAndView = new ModelAndView("UploadFile", model);
} else {
String folderStore = context.getInitParameter("path.to.upload.directory");
// MultipartFile file = command.getFile();
// MultipartFile file = command.getFileFromURL();
Log.info("URL = " + command.getFileURL());
Log.info("USE URL ? = " + command.getUseURL());
FileType fileType = getFileTypeService().findByID(command.getFileTypeId());
Integer id = getRequestedId(request);
String typeNode = getRequestedTypeNode(request);
Log.info("ID = " + id);
Log.info("typeNode = " + typeNode);
if ("st".equals(typeNode)) {
Study study = getStudyService().findByID(id);
getFileUploadService().uploadFile(study, command, fileType, registration);
}
if ("exp".equals(typeNode)) {
Experiment experiment = getExperimentService().findByID(id);
getFileUploadService().uploadFile(experiment, command, fileType, registration);
}
if ("sam".equals(typeNode)) {
Sample sample = getSampleService().findByID(id);
getFileUploadService().uploadFile(sample, command, fileType, registration);
}
if ("seq".equals(typeNode)) {
Lane lane = getLaneService().findByID(id);
getFileUploadService().uploadFile(lane, command, fileType, registration);
}
if ("ius".equals(typeNode)) {
IUS ius = getIUSService().findByID(id);
getFileUploadService().uploadFile(ius, command, fileType, registration);
}
if ("ae".equals(typeNode)) {
Processing processing = getProcessingService().findByID(id);
getFileUploadService().uploadFile(processing, command, fileType, registration);
}
if ("sr".equals(typeNode)) {
SequencerRun sequencerRun = getSequencerRunService().findByID(id);
getFileUploadService().uploadFile(sequencerRun, command, fileType, registration);
}
modelAndView = new ModelAndView(getViewName(request));
}
return modelAndView;
}
/**
* {@inheritDoc}
*
* @return
*/
@Override
@Put
public Representation put(Representation entity) {
authenticate();
Representation representation = null;
Lane newLane = null;
JaxbObject<Lane> jo = new JaxbObject<>();
try {
String text = entity.getText();
newLane = (Lane) XmlTools.unMarshal(jo, new Lane(), text);
} catch (SAXException | IOException ex) {
ex.printStackTrace();
throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
}
try {
LaneService fs = BeanFactory.getLaneServiceBean();
Lane lane = testIfNull(fs.findByID(newLane.getLaneId()));
lane.givesPermission(registration);
// simple types
String name = newLane.getName();
String desc = newLane.getDescription();
Integer laneIndex = newLane.getLaneIndex();
String cycleDescriptor = newLane.getCycleDescriptor();
Boolean skip = newLane.getSkip();
String tags = newLane.getTags();
String regions = newLane.getRegions();
// foreign keys
Sample sample = newLane.getSample();
Registration owner = newLane.getOwner();
Set<LaneAttribute> newAttributes = newLane.getLaneAttributes();
if (name != null) {
lane.setName(name);
}
if (desc != null) {
lane.setDescription(desc);
}
if (laneIndex != null) {
lane.setLaneIndex(laneIndex);
}
if (cycleDescriptor != null) {
lane.setCycleDescriptor(cycleDescriptor);
}
if (skip != null) {
lane.setSkip(skip);
}
if (tags != null) {
lane.setTags(tags);
}
if (regions != null) {
lane.setRegions(regions);
}
if (sample != null) {
SampleService ss = BeanFactory.getSampleServiceBean();
Sample newSample = ss.findByID(sample.getSampleId());
if (newSample != null && newSample.givesPermission(registration)) {
lane.setSample(newSample);
} else if (newSample == null) {
Log.info("Could not be found " + sample);
}
}
if (owner != null) {
RegistrationService rs = BeanFactory.getRegistrationServiceBean();
Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
if (newReg != null) {
lane.setOwner(newReg);
} else {
Log.info("Could not be found " + owner);
}
} else if (lane.getOwner() == null) {
lane.setOwner(registration);
}
if (newAttributes != null) {
// SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
LaneIDResource.mergeAttributes(lane.getLaneAttributes(), newAttributes, lane);
}
fs.update(registration, lane);
Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
Lane detachedLane =
copier.hibernate2dto(
Lane.class,
lane,
new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
new CollectionPropertyName<?>[] {});
Document line = XmlTools.marshalToDocument(jo, detachedLane);
representation = XmlTools.getRepresentation(line);
getResponse().setEntity(representation);
getResponse()
.setLocationRef(getRequest().getRootRef() + "/lanes/" + detachedLane.getSwAccession());
getResponse().setStatus(Status.SUCCESS_CREATED);
} catch (SecurityException e) {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
} catch (Exception e) {
e.printStackTrace();
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
}
return representation;
}
@Test
public void testPackageBundleAndInstallSeparately() throws IOException {
separateTempDir = Files.createTempDir();
Log.info("Trying to package archetype at: " + separateTempDir.getAbsolutePath());
PluginRunner it = new PluginRunner();
String SEQWARE_VERSION = it.getClass().getPackage().getImplementationVersion();
Assert.assertTrue("unable to detect seqware version", SEQWARE_VERSION != null);
Log.info("SeqWare version detected as: " + SEQWARE_VERSION);
File packageDir = Files.createTempDir();
// for this test, we're going to create, install and package just one archetype. Doing more
// seems redundant for this test
String[] archetypes = {
"java-workflow" /*, "simplified-ftl-workflow", "legacy-ftl-workflow", "simple-legacy-ftl-workflow"*/
};
for (String archetype : archetypes) {
String workflow = "seqware-archetype-" + archetype;
// generate and install archetypes to local maven repo
String command =
"mvn archetype:generate -DarchetypeCatalog=local -Dpackage=com.seqware.github -DgroupId=com.github.seqware -DarchetypeArtifactId="
+ workflow
+ " -Dversion=1.0-SNAPSHOT -DarchetypeGroupId=com.github.seqware -DartifactId="
+ workflow
+ " -DworkflowDirectoryName="
+ workflow
+ " -DworkflowName="
+ workflow
+ " -DworkflowVersion=1.0-SNAPSHOT -B -Dgoals=install";
String genOutput = ITUtility.runArbitraryCommand(command, 0, separateTempDir);
Log.info(genOutput);
// install the workflows to the database and record their information
File workflowDir = new File(separateTempDir, workflow);
File targetDir = new File(workflowDir, "target");
File bundleDir =
new File(
targetDir,
"Workflow_Bundle_" + workflow + "_1.0-SNAPSHOT_SeqWare_" + SEQWARE_VERSION);
String packageCommand =
"-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
+ packageDir
+ " -p "
+ bundleDir.getAbsolutePath();
String packageOutput = ITUtility.runSeqWareJar(packageCommand, ReturnValue.SUCCESS);
Log.info(packageOutput);
// locate the zip bundle and then install it
File zippedBundle = new File(packageDir, bundleDir.getName() + ".zip");
Assert.assertTrue(
"zipped bundle " + zippedBundle.getAbsolutePath() + ".zip", zippedBundle.exists());
String installCommand =
"-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
+ zippedBundle
+ " -i";
String installOutput = ITUtility.runSeqWareJar(installCommand, ReturnValue.SUCCESS);
Log.info(installOutput);
}
FileUtils.deleteDirectory(packageDir);
}
