Examples with Fit3DJobParameters bio.fkaiser.fit3d.web.model.Fit3DJobParameters used on opensource projects

Example 1 with Fit3DJobParameters

use of bio.fkaiser.fit3d.web.model.Fit3DJobParameters 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 Fit3DJobParameters

use of bio.fkaiser.fit3d.web.model.Fit3DJobParameters in project fit3d by fkaiserbio.

the class JobConverter method toDocument.

public static Document toDocument(Fit3DJob job) {
    Fit3DJobParameters parameters = job.getParameters();
    List<String> exchangeDefinitionStrings = parameters.getExchangeDefinitions().stream().map(ExchangeDefinition::toString).collect(Collectors.toList());
    Document parametersObject = new Document().append("atomFilterType", parameters.getAtomFilterType().toString()).append("pdbTargetList", parameters.isPdbTargetList()).append("chainTargetList", parameters.isChainTargetList()).append("targetListPath", parameters.getTargetListPath().toString()).append("motifPath", parameters.getMotifPath().toString()).append("statisticalModel", parameters.getStatisticalModelType().toString()).append("rmsdLimit", parameters.getRmsdLimit()).append("exchangeDefinitions", exchangeDefinitionStrings);
    return new Document().append("timeStamp", job.getTimeStamp().toString()).append("jobIdentifier", job.getJobIdentifier().toString()).append("sessionIdentifier", job.getSessionIdentifier().toString()).append("ipAddress", job.getIpAddress()).append("jobPath", job.getJobPath().toString()).append("description", job.getDescription()).append("email", job.getEmail()).append("enqueued", job.isEnqueued()).append("running", job.isRunning()).append("finished", job.isFinished()).append("failed", job.isFailed()).append("sendMail", job.isSendMail()).append("errorMessage", job.getErrorMessage()).append("parameters", parametersObject);
}

Example 3 with Fit3DJobParameters

use of bio.fkaiser.fit3d.web.model.Fit3DJobParameters 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;
}