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

Example 1 with UnknownEntityException

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

the class TagWizardController method viewTagWizard.

/**
 * Displays on tag wizard button press
 *
 * @param target The target entity name
 * @param model  the model
 * @return name of the tag wizard view
 */
@GetMapping
public String viewTagWizard(@RequestParam(required = false, value = "selectedTarget") String target, Model model) {
    List<String> entityTypeIds = dataService.findAll(ENTITY_TYPE_META_DATA, EntityType.class).map(EntityType::getId).collect(toList());
    if (StringUtils.isEmpty(target)) {
        Optional<String> findFirst = entityTypeIds.stream().findFirst();
        if (findFirst.isPresent()) {
            target = findFirst.get();
        }
    }
    if (StringUtils.isEmpty(target)) {
        throw new UnknownEntityException("There are no entities available!");
    }
    List<Ontology> ontologies = ontologyService.getOntologies();
    EntityType emd = dataService.getEntityType(target);
    List<Attribute> attributes = newArrayList(emd.getAttributes());
    Map<String, Multimap<Relation, OntologyTerm>> taggedAttributes = attributes.stream().collect(toMap((Attribute::getName), (x -> ontologyTagService.getTagsForAttribute(emd, x))));
    model.addAttribute("entity", emd);
    model.addAttribute("entityTypeIds", entityTypeIds);
    model.addAttribute("attributes", attributes);
    model.addAttribute("ontologies", ontologies);
    model.addAttribute("taggedAttributes", taggedAttributes);
    model.addAttribute("relations", Relation.values());
    return VIEW_TAG_WIZARD;
}

Example 2 with UnknownEntityException

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

the class UntypedTagService method getTagsForPackage.

@Override
@RunAsSystem
public Iterable<SemanticTag<Package, LabeledResource, LabeledResource>> getTagsForPackage(Package p) {
    Entity packageEntity = dataService.findOne(PACKAGE, new QueryImpl<>().eq(PackageMetadata.ID, p.getId()));
    if (packageEntity == null) {
        throw new UnknownEntityException("Unknown package [" + p.getId() + "]");
    }
    List<SemanticTag<Package, LabeledResource, LabeledResource>> tags = Lists.newArrayList();
    for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) {
        tags.add(SemanticTag.asTag(p, tagEntity));
    }
    return tags;
}

Example 3 with UnknownEntityException

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

the class OntologyTagServiceImpl method getTagsForPackage.

@Override
public Iterable<SemanticTag<Package, OntologyTerm, Ontology>> getTagsForPackage(Package package_) {
    Entity packageEntity = dataService.findOneById(PACKAGE, package_.getId());
    if (packageEntity == null) {
        throw new UnknownEntityException("Unknown package [" + package_.getId() + "]");
    }
    List<SemanticTag<Package, OntologyTerm, Ontology>> tags = Lists.newArrayList();
    for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) {
        tags.add(asTag(package_, tagEntity));
    }
    return tags;
}

Example 4 with UnknownEntityException

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

the class OntologyScriptInitializerImpl method initialize.

@Override
@RunAsSystem
public void initialize() {
    Resource resource = new ClassPathResource("roc-curve.R");
    if (resource.exists()) {
        long count = dataService.count(SCRIPT, new QueryImpl<>().eq(ScriptMetaData.NAME, ROC_CURVE_SCRIPT_NAME));
        if (count == 0) {
            Entity scriptType = dataService.findOne(ScriptTypeMetaData.SCRIPT_TYPE, new QueryImpl<>().eq(ScriptTypeMetaData.NAME, "R"));
            if (scriptType == null)
                throw new UnknownEntityException("ScriptType R does not exist!");
            String scriptContent;
            try {
                scriptContent = FileCopyUtils.copyToString(new InputStreamReader(resource.getInputStream(), "UTF-8"));
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
            if (dataService.count(SCRIPT_PARAMETER, new QueryImpl<>().eq(ScriptParameterMetaData.NAME, ROC_CURVE_SCRIPT_PARAMETER)) == 0) {
                dataService.add(SCRIPT_PARAMETER, scriptParameterFactory.create().setName(ROC_CURVE_SCRIPT_PARAMETER));
            }
            Entity scriptParameterEntity = dataService.findOne(SCRIPT_PARAMETER, new QueryImpl<>().eq(ScriptParameterMetaData.NAME, ROC_CURVE_SCRIPT_PARAMETER));
            Script script = scriptFactory.create();
            script.setName(ROC_CURVE_SCRIPT_NAME);
            script.setGenerateToken(true);
            script.set(ScriptMetaData.TYPE, scriptType);
            script.setResultFileExtension("png");
            script.setContent(scriptContent);
            script.set(ScriptMetaData.PARAMETERS, Arrays.asList(scriptParameterEntity));
            dataService.add(SCRIPT, script);
            LOG.info("Script entity \"roc\" has been added to the database!");
        } else {
            LOG.info("Script entity \"roc\" already exists in the database!");
        }
    } else {
        LOG.info("R script \"roc-curve.R\" does not exist on classpath!");
    }
}

Example 5 with UnknownEntityException

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

the class EntityMappingRepositoryImpl method toEntityMapping.

private EntityMapping toEntityMapping(Entity entityMappingEntity) {
    String identifier = entityMappingEntity.getString(EntityMappingMetaData.IDENTIFIER);
    EntityType targetEntityType;
    try {
        targetEntityType = dataService.getEntityType(entityMappingEntity.getString(EntityMappingMetaData.TARGET_ENTITY_TYPE));
    } catch (UnknownEntityException uee) {
        LOG.error(uee.getMessage());
        targetEntityType = null;
    }
    EntityType sourceEntityType;
    try {
        sourceEntityType = dataService.getEntityType(entityMappingEntity.getString(EntityMappingMetaData.SOURCE_ENTITY_TYPE));
    } catch (UnknownEntityException uee) {
        LOG.error(uee.getMessage());
        sourceEntityType = null;
    }
    List<Entity> attributeMappingEntities = Lists.newArrayList(entityMappingEntity.getEntities(EntityMappingMetaData.ATTRIBUTE_MAPPINGS));
    List<AttributeMapping> attributeMappings = attributeMappingRepository.getAttributeMappings(attributeMappingEntities, sourceEntityType, targetEntityType);
    return new EntityMapping(identifier, sourceEntityType, targetEntityType, attributeMappings);
}