Examples with RetentionTimeNotFoundException de.ipbhalle.metfraglib.exceptions.RetentionTimeNotFoundException used on opensource projects

Example 1 with RetentionTimeNotFoundException

use of de.ipbhalle.metfraglib.exceptions.RetentionTimeNotFoundException in project MetFragRelaunched by ipb-halle.

the class BeanSettingsContainer method preprocessRetentionTimeTrainingFile.

public void preprocessRetentionTimeTrainingFile() throws Exception {
    if (this.retentionTimeScoreTrainingFilePath == null || this.retentionTimeScoreTrainingFilePath.trim().length() == 0)
        return;
    if (this.availableCandidatePartitioningCoefficients == null || this.availableCandidatePartitioningCoefficients.size() == 0)
        return;
    java.io.File retentionTimeTrainingFile = new java.io.File(this.retentionTimeScoreTrainingFilePath);
    if (retentionTimeTrainingFile != null && retentionTimeTrainingFile.exists() && retentionTimeTrainingFile.canRead()) {
        MetFragGlobalSettings settings = new MetFragGlobalSettings();
        settings.set(VariableNames.LOG_LEVEL_NAME, Level.DEBUG);
        settings.set(VariableNames.METFRAG_DATABASE_TYPE_NAME, "LocalProperty");
        settings.set(VariableNames.LOCAL_DATABASE_PATH_NAME, this.retentionTimeScoreTrainingFilePath);
        CombinedMetFragProcess combinedMetFragProcess = new CombinedMetFragProcess(settings);
        boolean entriesRetrieved = combinedMetFragProcess.retrieveCompounds();
        if (entriesRetrieved) {
            CandidateList candidates = combinedMetFragProcess.getCandidateList();
            if (candidates == null || candidates.getNumberElements() <= 1)
                throw new TooFewCandidatesException();
            if (!candidates.getElement(0).getProperties().containsKey(VariableNames.RETENTION_TIME_NAME))
                throw new RetentionTimeNotFoundException();
            this.availablePartitioningCoefficients = new java.util.ArrayList<SelectItem>();
            java.util.Enumeration<String> keys = candidates.getElement(0).getProperties().keys();
            while (keys.hasMoreElements()) {
                String currentKey = keys.nextElement().trim();
                if (currentKey.equals(VariableNames.INCHI_NAME)) {
                    currentKey = "CDK";
                }
                for (int k = 0; k < this.availableCandidatePartitioningCoefficients.size(); k++) {
                    if (this.availableCandidatePartitioningCoefficients.get(k).getLabel().equals(currentKey)) {
                        if (currentKey.equals("CDK"))
                            this.availablePartitioningCoefficients.add(new SelectItem(currentKey));
                        else {
                            if (this.isValidLogValueProperty(currentKey, candidates))
                                this.availablePartitioningCoefficients.add(new SelectItem(currentKey));
                        }
                    }
                }
            }
        }
        Collections.sort(this.availablePartitioningCoefficients, new java.util.Comparator<SelectItem>() {

            @Override
            public int compare(SelectItem left, SelectItem right) {
                return ((String) left.getValue()).compareTo((String) right.getValue());
            }
        });
    } else
        this.availablePartitioningCoefficients = null;
}

Example 2 with RetentionTimeNotFoundException

use of de.ipbhalle.metfraglib.exceptions.RetentionTimeNotFoundException in project MetFragRelaunched by ipb-halle.

the class UserInputDataHandler method handleRetentionTimeTrainingFile.

/**
 * @param retentionTimeTrainingFile
 * @param infoMessages
 * @param errorMessages
 * @return
 */
public void handleRetentionTimeTrainingFile(UploadedFile retentionTimeTrainingFile, Messages infoMessages, Messages errorMessages, BeanSettingsContainer beanSettingsContainer) {
    if (retentionTimeTrainingFile == null) {
        errorMessages.setMessage("retentionTimeTrainingFileError", "Error: Retention time training file was not saved.");
        return;
    }
    // create upload folder
    File uploadFolder = this.fileStorer.prepareFolder(beanSettingsContainer.getRootSessionFolder() + Constants.OS_SPECIFIC_FILE_SEPARATOR + "retentiontimescore", errorMessages);
    if (uploadFolder == null)
        return;
    // store the file
    File storedFile = null;
    try {
        storedFile = this.fileStorer.saveUploadedFile(retentionTimeTrainingFile, uploadFolder);
        beanSettingsContainer.setRetentionTimeScoreTrainingFilePath(storedFile.getAbsolutePath());
    } catch (Exception e) {
        errorMessages.setMessage("retentionTimeTrainingFileError", "Error: Retention time training file was not saved.");
        beanSettingsContainer.setRetentionTimeScoreTrainingFilePath("");
        return;
    }
    // preprocess
    try {
        beanSettingsContainer.preprocessRetentionTimeTrainingFile();
        if (beanSettingsContainer.getAvailablePartitioningCoefficients() == null || beanSettingsContainer.getAvailablePartitioningCoefficients().size() == 0) {
            errorMessages.setMessage("retentionTimeTrainingFileError", "No proper value for a partitioning coefficient found. Check candidate and retention time file.");
            beanSettingsContainer.setScoreValid(false, "retentionTimeTrainingFile");
            beanSettingsContainer.setRetentionTimeScoreTrainingFilePath("");
            return;
        }
    } catch (TooFewCandidatesException e1) {
        beanSettingsContainer.setScoreValid(false, "retentionTimeTrainingFile");
        beanSettingsContainer.setRetentionTimeScoreTrainingFilePath("");
        beanSettingsContainer.setAvailablePartitioningCoefficients(null);
        errorMessages.setMessage("retentionTimeTrainingFileError", "Error: Uploaded file contains too few values.");
    } catch (RetentionTimeNotFoundException e2) {
        beanSettingsContainer.setScoreValid(false, "retentionTimeTrainingFile");
        beanSettingsContainer.setRetentionTimeScoreTrainingFilePath("");
        beanSettingsContainer.setAvailablePartitioningCoefficients(null);
        errorMessages.setMessage("retentionTimeTrainingFileError", "Error: Uploaded file does not contain a RetentionTime field.");
    } catch (Exception e3) {
        e3.printStackTrace();
        beanSettingsContainer.setScoreValid(false, "retentionTimeTrainingFile");
        beanSettingsContainer.setRetentionTimeScoreTrainingFilePath("");
        beanSettingsContainer.setAvailablePartitioningCoefficients(null);
        errorMessages.setMessage("retentionTimeTrainingFileError", "Error: Could not read file. Missing/Wrong header?");
    }
}