Examples with MolgenisDataException org.molgenis.data.MolgenisDataException used on opensource projects

Example 26 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class JobScheduler method runNow.

/**
 * Executes a {@link ScheduledJob} immediately.
 *
 * @param scheduledJobId ID of the {@link ScheduledJob} to run
 */
public synchronized void runNow(String scheduledJobId) {
    ScheduledJob scheduledJob = getJob(scheduledJobId);
    try {
        JobKey jobKey = new JobKey(scheduledJobId, SCHEDULED_JOB_GROUP);
        if (quartzScheduler.checkExists(jobKey)) {
            // Run job now
            quartzScheduler.triggerJob(jobKey);
        } else {
            // Schedule with 'now' trigger
            Trigger trigger = newTrigger().withIdentity(scheduledJobId, SCHEDULED_JOB_GROUP).startNow().build();
            schedule(scheduledJob, trigger);
        }
    } catch (SchedulerException e) {
        LOG.error("Error runNow ScheduledJob", e);
        throw new MolgenisDataException("Error job runNow", e);
    }
}

Example 27 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class PostgreSqlUtils method getPostgreSqlQueryValue.

/**
 * Returns the PostgreSQL query value for the given entity attribute. For query operators requiring a list of
 * values (e.g. IN or RANGE) this method must be called for each individual query value.
 *
 * @param queryValue value of the type that matches the attribute type
 * @param attr       attribute
 * @return PostgreSQL value
 */
static Object getPostgreSqlQueryValue(Object queryValue, Attribute attr) {
    while (true) {
        String attrName = attr.getName();
        AttributeType attrType = attr.getDataType();
        switch(attrType) {
            case BOOL:
                if (queryValue != null && !(queryValue instanceof Boolean)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Boolean.class.getSimpleName()));
                }
                return queryValue;
            case CATEGORICAL:
            // one query value
            case CATEGORICAL_MREF:
            case FILE:
            // one query value
            case MREF:
            case XREF:
            case ONE_TO_MANY:
                // queries values referencing an entity can either be the entity itself or the entity id
                if (queryValue != null) {
                    if (queryValue instanceof Entity) {
                        queryValue = ((Entity) queryValue).getIdValue();
                    }
                    attr = attr.getRefEntity().getIdAttribute();
                    continue;
                } else {
                    return null;
                }
            case DATE:
                if (queryValue != null && !(queryValue instanceof LocalDate)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), LocalDate.class.getSimpleName()));
                }
                return queryValue;
            case DATE_TIME:
                if (queryValue == null) {
                    return null;
                }
                if (!(queryValue instanceof Instant)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Instant.class.getSimpleName()));
                }
                return ((Instant) queryValue).atOffset(UTC);
            case DECIMAL:
                if (queryValue != null && !(queryValue instanceof Double)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Double.class.getSimpleName()));
                }
                return queryValue;
            case ENUM:
                // enum query values can be an enum or enum string
                if (queryValue != null) {
                    if (queryValue instanceof String) {
                        return queryValue;
                    } else if (queryValue instanceof Enum<?>) {
                        return queryValue.toString();
                    } else {
                        throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s] or [%s]", attrName, queryValue.getClass().getSimpleName(), String.class.getSimpleName(), Enum.class.getSimpleName()));
                    }
                } else {
                    return null;
                }
            case EMAIL:
            case HTML:
            case HYPERLINK:
            case SCRIPT:
            case STRING:
            case TEXT:
                if (queryValue != null && !(queryValue instanceof String)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), String.class.getSimpleName()));
                }
                return queryValue;
            case INT:
                if (queryValue != null && !(queryValue instanceof Integer)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Integer.class.getSimpleName()));
                }
                return queryValue;
            case LONG:
                if (queryValue != null && !(queryValue instanceof Long)) {
                    throw new MolgenisDataException(format("Attribute [%s] query value is of type [%s] instead of [%s]", attrName, queryValue.getClass().getSimpleName(), Long.class.getSimpleName()));
                }
                return queryValue;
            case COMPOUND:
                throw new RuntimeException(format("Illegal attribute type [%s]", attrType.toString()));
            default:
                throw new UnexpectedEnumException(attrType);
        }
    }
}

Example 28 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class MappingProjectRepositoryImpl method update.

@Override
@Transactional
public void update(MappingProject mappingProject) {
    MappingProject existing = getMappingProject(mappingProject.getIdentifier());
    if (existing == null) {
        throw new MolgenisDataException("MappingProject does not exist");
    }
    Entity mappingProjectEntity = toEntity(mappingProject);
    dataService.update(MAPPING_PROJECT, mappingProjectEntity);
}

Example 29 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class FileRepositoryCollectionFactory method createFileRepositoryCollection.

/**
 * Factory method for creating a new FileRepositorySource
 * <p>
 * For example an excel file
 */
public FileRepositoryCollection createFileRepositoryCollection(File file) {
    Class<? extends FileRepositoryCollection> clazz;
    String extension = FileExtensionUtils.findExtensionFromPossibilities(file.getName(), fileRepositoryCollection.keySet());
    clazz = fileRepositoryCollection.get(extension);
    if (clazz == null) {
        throw new MolgenisDataException("Unknown extension for file '" + file.getName() + "'");
    }
    Constructor<? extends FileRepositoryCollection> ctor;
    try {
        ctor = clazz.getConstructor(File.class);
    } catch (Exception e) {
        throw new MolgenisDataException("Exception creating [" + clazz + "]  missing constructor FileRepositorySource(File file)");
    }
    FileRepositoryCollection fileRepositoryCollection = BeanUtils.instantiateClass(ctor, file);
    autowireCapableBeanFactory.autowireBeanProperties(fileRepositoryCollection, AutowireCapableBeanFactory.AUTOWIRE_BY_TYPE, false);
    try {
        fileRepositoryCollection.init();
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
    return fileRepositoryCollection;
}

Example 30 with MolgenisDataException

use of org.molgenis.data.MolgenisDataException in project molgenis by molgenis.

the class ImportRunService method createAndSendStatusMail.

private void createAndSendStatusMail(ImportRun importRun) {
    try {
        SimpleMailMessage mailMessage = new SimpleMailMessage();
        mailMessage.setTo(userService.getUser(importRun.getUsername()).getEmail());
        mailMessage.setSubject(createMailTitle(importRun));
        mailMessage.setText(createEnglishMailText(importRun, ZoneId.systemDefault()));
        mailSender.send(mailMessage);
    } catch (MailException mce) {
        LOG.error("Could not send import status mail", mce);
        throw new MolgenisDataException("An error occurred. Please contact the administrator.");
    }
}