Examples with Fit3DJob bio.fkaiser.fit3d.web.model.Fit3DJob used on opensource projects

Example 1 with Fit3DJob

use of bio.fkaiser.fit3d.web.model.Fit3DJob in project fit3d by fkaiserbio.

the class SubmitJobView method submit.

public String submit() {
    // determine if too many jobs were submitted in current session
    int jobCount = getJobCountOfCurrentSession();
    if (jobCount > Fit3DWebConstants.JOB_LIMIT) {
        FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error", "Too many jobs submitted. Please wait until until some jobs are finished.");
        FacesContext.getCurrentInstance().addMessage(null, message);
        return null;
    }
    // determine if too many exchanges were defined
    if (exchangeDefinitions != null) {
        int exchangeCount = (int) exchangeDefinitions.stream().map(ExchangeDefinition::getExchangeAminoAcids).mapToLong(Collection::size).sum();
        if (exchangeCount > Fit3DWebConstants.EXCHANGE_LIMIT) {
            FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error", "Only " + Fit3DWebConstants.EXCHANGE_LIMIT + " PSEs are allowed. Please use the command line or API version for more complex calculations.");
            FacesContext.getCurrentInstance().addMessage(null, message);
            return null;
        }
    }
    // motif file upload is mandatory
    if (!motifFileUploaded) {
        FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error", "A motif file is required.");
        FacesContext.getCurrentInstance().addMessage(null, message);
        return null;
    }
    // use predefined target list if no one was provided
    if (!targetListFileUploaded) {
        if (predefinedList == PredefinedList.NONE) {
            FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error", "Please select or upload a target list.");
            FacesContext.getCurrentInstance().addMessage(null, message);
            return null;
        } else {
            targetListPath = predefinedList.getPath();
            chainTargetList = true;
        }
    }
    Fit3DJobParameters jobParameters = new Fit3DJobParameters();
    jobParameters.setAtomFilterType(atomFilterType);
    jobParameters.setChainTargetList(chainTargetList);
    jobParameters.setPdbTargetList(pdbTargetList);
    if (motifPath.endsWith("4cha_motif.pdb")) {
        targetListPath = motifPath.getParent().resolve("targets.txt");
        logger.info("example run detected, using short target list {}", targetListPath);
        motifPath = motifPath.getParent().resolve("4cha_motif.pdb");
    }
    jobParameters.setMotifPath(motifPath);
    jobParameters.setTargetListPath(targetListPath);
    jobParameters.setRmsdLimit(rmsdLimit);
    jobParameters.setExchangeDefinitions(exchangeDefinitions);
    jobParameters.setStatisticalModelType(statisticalModelType);
    Fit3DJob job = new Fit3DJob(jobIdentifier, sessionManager.getSessionIdentifier(), determineIpAddress(), description, email, jobPath, jobParameters);
    FacesContext facesContext = FacesContext.getCurrentInstance();
    Flash flash = facesContext.getExternalContext().getFlash();
    flash.put("job", job);
    return "success";
}

Example 2 with Fit3DJob

use of bio.fkaiser.fit3d.web.model.Fit3DJob in project fit3d by fkaiserbio.

the class JobManager method cancelJob.

public void cancelJob(Fit3DJob job) {
    UUID jobIdentifier = job.getJobIdentifier();
    Optional<Fit3DJob> optionalJob = managedJobs.values().stream().flatMap(Collection::stream).filter(managedJob -> managedJob.getJobIdentifier().equals(jobIdentifier)).findFirst();
    optionalJob.ifPresent(Fit3DJob::cancel);
    if (optionalJob.isPresent()) {
        Fit3DJob managedJob = optionalJob.get();
        managedJob.cancel();
        logger.info("sent cancel signal to job {}", managedJob);
    } else {
        logger.info("job with identifier not found {}", job.getJobIdentifier());
    }
}

Example 3 with Fit3DJob

use of bio.fkaiser.fit3d.web.model.Fit3DJob in project fit3d by fkaiserbio.

the class JobManager method addJob.

public void addJob(Fit3DJob job) {
    Document jobObject = JobConverter.toDocument(job);
    mongoCollection.insertOne(jobObject);
    jobLoadManager.updateTotalJobs();
    logger.info("new job {} added to database", job);
    // add jobs to existing jobs of current session
    UUID sessionIdentifier = job.getSessionIdentifier();
    if (managedJobs.containsKey(sessionIdentifier)) {
        managedJobs.get(sessionIdentifier).add(job);
    } else {
        List<Fit3DJob> jobs = new ArrayList<>();
        jobs.add(job);
        managedJobs.put(sessionIdentifier, jobs);
    }
    // enqueue new job for execution
    Future<?> future = jobExecutor.enqueue(job);
    job.setFuture(future);
}

Example 4 with Fit3DJob

use of bio.fkaiser.fit3d.web.model.Fit3DJob in project fit3d by fkaiserbio.

the class AdminView method init.

@PostConstruct
public void init() {
    MongoClient mongoClient = new MongoClient(Fit3DWebConstants.Database.DB_HOST, Fit3DWebConstants.Database.DB_PORT);
    MongoCollection<Document> mongoCollection = mongoClient.getDatabase(Fit3DWebConstants.Database.DB_NAME).getCollection(Fit3DWebConstants.Database.DB_COLLECTION_NAME);
    FindIterable<Document> documents = mongoCollection.find();
    jobs = new ArrayList<>();
    for (Document document : documents) {
        Fit3DJob job = JobConverter.toFit3DJob(document);
        jobs.add(job);
    }
}

Example 5 with Fit3DJob

use of bio.fkaiser.fit3d.web.model.Fit3DJob in project fit3d by fkaiserbio.

the class JobConverter method toFit3DJob.

@SuppressWarnings("unchecked")
public static Fit3DJob toFit3DJob(Document jobDocument) {
    Document parametersObject = (Document) jobDocument.get("parameters");
    List<ExchangeDefinition> exchangeDefinitions = ((List<String>) parametersObject.get("exchangeDefinitions")).stream().map(ExchangeDefinition::fromString).collect(Collectors.toList());
    Fit3DJobParameters parameters = new Fit3DJobParameters();
    parameters.setAtomFilterType(AtomFilterType.valueOf((String) parametersObject.get("atomFilterType")));
    parameters.setPdbTargetList((boolean) parametersObject.get("pdbTargetList"));
    parameters.setChainTargetList((boolean) parametersObject.get("chainTargetList"));
    parameters.setTargetListPath(Paths.get((String) parametersObject.get("targetListPath")));
    parameters.setMotifPath(Paths.get((String) parametersObject.get("motifPath")));
    parameters.setStatisticalModelType(StatisticalModelType.valueOf((String) parametersObject.get("statisticalModel")));
    parameters.setRmsdLimit((double) parametersObject.get("rmsdLimit"));
    parameters.setExchangeDefinitions(exchangeDefinitions);
    Fit3DJob fit3dJob = new Fit3DJob();
    fit3dJob.setTimeStamp(LocalDateTime.parse((String) jobDocument.get("timeStamp")));
    fit3dJob.setSessionIdentifier((UUID.fromString((String) jobDocument.get("sessionIdentifier"))));
    fit3dJob.setIpAddress((String) jobDocument.get("ipAddress"));
    fit3dJob.setJobIdentifier(UUID.fromString((String) jobDocument.get("jobIdentifier")));
    fit3dJob.setJobPath(Paths.get((String) jobDocument.get("jobPath")));
    fit3dJob.setDescription((String) jobDocument.get("description"));
    fit3dJob.setEmail((String) jobDocument.get("email"));
    fit3dJob.setEnqueued((boolean) jobDocument.get("enqueued"));
    fit3dJob.setRunning((boolean) jobDocument.get("running"));
    fit3dJob.setFinished((boolean) jobDocument.get("finished"));
    fit3dJob.setFailed((boolean) jobDocument.get("failed"));
    fit3dJob.setSendMail((boolean) jobDocument.get("sendMail"));
    fit3dJob.setErrorMessage((String) jobDocument.get("errorMessage"));
    fit3dJob.setParameters(parameters);
    return fit3dJob;
}