Examples with Package org.molgenis.data.meta.model.Package used on opensource projects

Example 1 with Package

use of org.molgenis.data.meta.model.Package in project molgenis by molgenis.

the class EmxMetaDataParser method buildValidationReport.

private EntitiesValidationReport buildValidationReport(RepositoryCollection source, MyEntitiesValidationReport report, Map<String, EntityType> metaDataMap) {
    metaDataMap.values().forEach(entityTypeValidator::validate);
    metaDataMap.values().stream().map(EntityType::getAllAttributes).forEach(attributes -> attributes.forEach(attr -> {
        attributeValidator.validate(attr, ValidationMode.ADD_SKIP_ENTITY_VALIDATION);
    }));
    // validate package/entity/attribute tags
    metaDataMap.values().stream().map(EntityType::getPackage).filter(Objects::nonNull).forEach(package_ -> package_.getTags().forEach(tagValidator::validate));
    metaDataMap.values().forEach(entityType -> entityType.getTags().forEach(tagValidator::validate));
    metaDataMap.values().stream().map(EntityType::getAllAttributes).forEach(attributes -> attributes.forEach(attr -> {
        attr.getTags().forEach(tagValidator::validate);
    }));
    report = generateEntityValidationReport(source, report, metaDataMap);
    // Add entities without data
    for (String entityTypeId : metaDataMap.keySet()) {
        if (!report.getSheetsImportable().containsKey(entityTypeId))
            report.addEntity(entityTypeId, true);
    }
    return report;
}

Example 2 with Package

use of org.molgenis.data.meta.model.Package in project molgenis by molgenis.

the class EmxMetaDataParser method parsePackagesSheet.

/**
 * Parses the packages sheet
 *
 * @param repo                {@link Repository} for the packages
 * @param intermediateResults {@link IntermediateParseResults} containing the parsed tag entities
 */
private void parsePackagesSheet(Repository<Entity> repo, IntermediateParseResults intermediateResults) {
    if (repo == null)
        return;
    // Collect packages
    int rowIndex = 1;
    for (Entity packageEntity : resolvePackages(repo)) {
        rowIndex++;
        // Package name is required
        String name = packageEntity.getString(EMX_PACKAGE_NAME);
        if (name == null)
            throw new IllegalArgumentException("package.name is missing on line " + rowIndex);
        Package package_ = packageFactory.create(name);
        package_.setDescription(packageEntity.getString(EMX_PACKAGE_DESCRIPTION));
        String label = packageEntity.getString(EMX_PACKAGE_LABEL);
        if (label == null) {
            label = name;
        }
        package_.setLabel(label);
        // Set parent package
        String parentName = packageEntity.getString(EMX_PACKAGE_PARENT);
        if (parentName != null) {
            if (!name.toLowerCase().startsWith(parentName.toLowerCase()))
                throw new MolgenisDataException("Inconsistent package structure. Package: '" + name + "', parent: '" + parentName + '\'');
            package_.setParent(intermediateResults.getPackage(parentName));
        }
        // Set package tags
        List<String> tagIdentifiers = toList(packageEntity.getString(EMX_PACKAGE_TAGS));
        if (tagIdentifiers != null && !tagIdentifiers.isEmpty()) {
            List<Tag> tags = toTags(intermediateResults, tagIdentifiers);
            package_.setTags(tags);
        }
        // Add the complete package to the parse results
        intermediateResults.addPackage(name, package_);
    }
}

Example 3 with Package

use of org.molgenis.data.meta.model.Package in project molgenis by molgenis.

the class IntermediateParseResults method addEntityType.

public EntityType addEntityType(String fullyQualifiedName) {
    String entityTypeLabel = fullyQualifiedName;
    Package pack = null;
    for (Package p : packages.values()) {
        String packageName = p.getId();
        if (fullyQualifiedName.toLowerCase().startsWith(packageName.toLowerCase())) {
            // package_entity
            entityTypeLabel = fullyQualifiedName.substring(packageName.length() + 1);
            pack = p;
        }
    }
    String entityTypeId;
    if (pack == null) {
        pack = this.defaultPackage;
        entityTypeId = DefaultPackage.PACKAGE_DEFAULT + Package.PACKAGE_SEPARATOR + fullyQualifiedName;
    } else {
        entityTypeId = fullyQualifiedName;
    }
    EntityType emd = entityTypeFactory.create(entityTypeId).setLabel(entityTypeLabel).setPackage(pack);
    entities.put(fullyQualifiedName, emd);
    return emd;
}

Example 4 with Package

use of org.molgenis.data.meta.model.Package in project molgenis by molgenis.

the class EntityTypeUtilsTest method isSystemEntityNotASystemIfNotInSystemPackage.

@Test
public void isSystemEntityNotASystemIfNotInSystemPackage() {
    EntityType entity = mock(EntityType.class);
    Package entityPackage = mock(Package.class);
    when(entity.getPackage()).thenReturn(entityPackage);
    when(entityPackage.getId()).thenReturn("not-system");
    when(entity.getId()).thenReturn("foo_bar_Entity");
    assertFalse(EntityTypeUtils.isSystemEntity(entity));
}

Example 5 with Package

use of org.molgenis.data.meta.model.Package in project molgenis by molgenis.

the class EntityTypeUtilsTest method buildFullNamePackage.

@Test
public void buildFullNamePackage() {
    Package package_ = when(mock(Package.class).getId()).thenReturn("my_first_package").getMock();
    assertEquals(EntityTypeUtils.buildFullName(package_, "simpleName"), "my_first_package_simpleName");
}