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

Example 36 with Attribute

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

the class QueryGeneratorReferencesTest method setUp.

@BeforeMethod
public void setUp() {
    EntityType refEntityType = entityTypeFactory.create("ref_entity");
    String refIdAttributeName = "xid";
    refEntityType.addAttribute(attrFactory.create().setName(refIdAttributeName), ROLE_ID);
    refEntityType.addAttribute(attrFactory.create().setName(refBoolAttributeName).setDataType(BOOL));
    refEntityType.addAttribute(attrFactory.create().setName(refCategoricalAttributeName).setDataType(CATEGORICAL).setRefEntity(refEntityType).setNillable(true));
    Attribute attrCompound = attrFactory.create().setName(refCompoundAttributeName).setDataType(COMPOUND);
    Attribute compoundPart0Attribute = attrFactory.create().setName(refCompoundPart0AttributeName).setDataType(STRING).setParent(attrCompound);
    String refCompoundPart1AttributeName = "xcompoundpart1";
    Attribute compoundPart1Attribute = attrFactory.create().setName(refCompoundPart1AttributeName).setDataType(STRING).setParent(attrCompound);
    refEntityType.addAttribute(attrCompound);
    refEntityType.addAttribute(compoundPart0Attribute);
    refEntityType.addAttribute(compoundPart1Attribute);
    refEntityType.addAttribute(attrFactory.create().setName(refDateAttributeName).setDataType(DATE));
    refEntityType.addAttribute(attrFactory.create().setName(refDateTimeAttributeName).setDataType(DATE_TIME));
    refEntityType.addAttribute(attrFactory.create().setName(refDecimalAttributeName).setDataType(DECIMAL));
    String refEmailAttributeName = "xemail";
    refEntityType.addAttribute(attrFactory.create().setName(refEmailAttributeName).setDataType(EMAIL));
    String refEnumAttributeName = "xenum";
    refEntityType.addAttribute(attrFactory.create().setName(refEnumAttributeName).setDataType(ENUM).setEnumOptions(Arrays.asList("enum0", "enum1", "enum2")));
    String refHtmlAttributeName = "xhtml";
    refEntityType.addAttribute(attrFactory.create().setName(refHtmlAttributeName).setDataType(HTML));
    String refHyperlinkAttributeName = "xhyperlink";
    refEntityType.addAttribute(attrFactory.create().setName(refHyperlinkAttributeName).setDataType(HYPERLINK));
    refEntityType.addAttribute(attrFactory.create().setName(refIntAttributeName).setDataType(INT));
    refEntityType.addAttribute(attrFactory.create().setName(refLongAttributeName).setDataType(LONG));
    String refMrefAttributeName = "xmref";
    refEntityType.addAttribute(attrFactory.create().setName(refMrefAttributeName).setDataType(MREF).setRefEntity(refEntityType).setNillable(true));
    String refScriptAttributeName = "xscript";
    refEntityType.addAttribute(attrFactory.create().setName(refScriptAttributeName).setDataType(SCRIPT));
    refEntityType.addAttribute(attrFactory.create().setName(refStringAttributeName).setDataType(STRING));
    String refTextAttributeName = "xtext";
    refEntityType.addAttribute(attrFactory.create().setName(refTextAttributeName).setDataType(TEXT));
    String refXrefAttributeName = "xxref";
    refEntityType.addAttribute(attrFactory.create().setName(refXrefAttributeName).setDataType(XREF).setRefEntity(refEntityType).setNillable(true));
    EntityType emd = entityTypeFactory.create("entity");
    String idAttributeName = "id";
    emd.addAttribute(attrFactory.create().setName(idAttributeName), ROLE_ID);
    emd.addAttribute(attrFactory.create().setName(stringAttributeName).setUnique(true), ROLE_LABEL);
    String mrefAttributeName = "mref";
    emd.addAttribute(attrFactory.create().setName(mrefAttributeName).setDataType(MREF).setNillable(true).setRefEntity(refEntityType));
    this.entityType = emd;
    DocumentIdGenerator documentIdGenerator = mock(DocumentIdGenerator.class);
    when(documentIdGenerator.generateId(any(Attribute.class))).thenAnswer(invocation -> ((Attribute) invocation.getArguments()[0]).getName());
    queryGenerator = new QueryGenerator(documentIdGenerator);
}

Example 37 with Attribute

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

the class AnnotatorDependencyOrderResolverTest method beforeMethod.

@BeforeMethod
public void beforeMethod() {
    Attribute attra = attributeFactory.create().setName("A").setDataType(STRING);
    // to check for matching "STRING" attributes to required "TEXT" attributes
    Attribute attra2 = attributeFactory.create().setName("A").setDataType(TEXT);
    Attribute attrb = attributeFactory.create().setName("B").setDataType(STRING);
    Attribute attrc = attributeFactory.create().setName("C").setDataType(STRING);
    Attribute attrd = attributeFactory.create().setName("D").setDataType(STRING);
    Attribute attre = attributeFactory.create().setName("E").setDataType(STRING);
    Attribute attrf = attributeFactory.create().setName("F").setDataType(STRING);
    Attribute attrg = attributeFactory.create().setName("G").setDataType(STRING);
    Attribute attrh = attributeFactory.create().setName("H").setDataType(STRING);
    Attribute attri = attributeFactory.create().setName("I").setDataType(STRING);
    Attribute attrj = attributeFactory.create().setName("J").setDataType(STRING);
    EntityType emd = entityTypeFactory.create("test");
    emd.addAttributes(Arrays.asList(attra, attrb));
    when(repo.getEntityType()).thenReturn(emd);
    when(annotator1.getInfo()).thenReturn(annotator1info);
    when(annotator2.getInfo()).thenReturn(annotator2info);
    when(annotator3.getInfo()).thenReturn(annotator3info);
    when(annotator4.getInfo()).thenReturn(annotator4info);
    when(annotator5.getInfo()).thenReturn(annotator5info);
    when(annotator1.getSimpleName()).thenReturn("annotator1");
    when(annotator2.getSimpleName()).thenReturn("annotator2");
    when(annotator3.getSimpleName()).thenReturn("annotator3");
    when(annotator4.getSimpleName()).thenReturn("annotator4");
    when(annotator5.getSimpleName()).thenReturn("annotator5");
    when(annotator1.getRequiredAttributes()).thenReturn(Arrays.asList(attrd, attrh, attri));
    when(annotator1info.getOutputAttributes()).thenReturn(Arrays.asList(attre, attrc));
    when(annotator2.getRequiredAttributes()).thenReturn(Arrays.asList(attra2, attrb));
    when(annotator2info.getOutputAttributes()).thenReturn(Arrays.asList(attrj));
    when(annotator3.getRequiredAttributes()).thenReturn(Arrays.asList(attra2, attrh));
    when(annotator3info.getOutputAttributes()).thenReturn(Arrays.asList(attrd, attrj));
    when(annotator4.getRequiredAttributes()).thenReturn(Arrays.asList(attra, attrb));
    when(annotator4info.getOutputAttributes()).thenReturn(Arrays.asList(attrh));
    when(annotator5.getRequiredAttributes()).thenReturn(Arrays.asList(attrb, attrd));
    when(annotator5info.getOutputAttributes()).thenReturn(Arrays.asList(attri, attrf));
}

Example 38 with Attribute

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

the class CsvRepository method getEntityType.

public EntityType getEntityType() {
    if (entityType == null) {
        entityType = entityTypeFactory.create(sheetName);
        for (String attrName : new CsvIterator(file, sheetName, null, separator).getColNamesMap().keySet()) {
            Attribute attr = attrMetaFactory.create().setName(attrName).setDataType(STRING);
            entityType.addAttribute(attr);
        }
    }
    return entityType;
}

Example 39 with Attribute

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

the class CsvWriter method writeAttributes.

/**
 * Use attribute labels as column names
 */
public void writeAttributes(Iterable<Attribute> attributes) throws IOException {
    List<String> attributeNames = Lists.newArrayList();
    List<String> attributeLabels = Lists.newArrayList();
    for (Attribute attr : attributes) {
        attributeNames.add(attr.getName());
        if (attr.getLabel() != null) {
            attributeLabels.add(attr.getLabel());
        } else {
            attributeLabels.add(attr.getName());
        }
    }
    writeAttributes(attributeNames, attributeLabels);
}

Example 40 with Attribute

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

the class QueryGenerator method createQueryClauseEqualsNoValue.

private QueryBuilder createQueryClauseEqualsNoValue(QueryRule queryRule, EntityType entityType) {
    List<Attribute> attributePath = getAttributePath(queryRule.getField(), entityType);
    String fieldName = getQueryFieldName(attributePath);
    Attribute attr = attributePath.get(0);
    AttributeType attrType = attr.getDataType();
    switch(attrType) {
        case BOOL:
        case DATE:
        case DATE_TIME:
        case DECIMAL:
        case EMAIL:
        case ENUM:
        case HTML:
        case HYPERLINK:
        case INT:
        case LONG:
        case SCRIPT:
        case STRING:
        case TEXT:
            return QueryBuilders.boolQuery().mustNot(QueryBuilders.existsQuery(fieldName));
        case CATEGORICAL:
        case CATEGORICAL_MREF:
        case FILE:
        case MREF:
        case ONE_TO_MANY:
        case XREF:
            if (attributePath.size() > 1) {
                throw new MolgenisQueryException("Can not filter on references deeper than 1.");
            }
            Attribute refIdAttr = attr.getRefEntity().getIdAttribute();
            List<Attribute> refAttributePath = concat(attributePath.stream(), of(refIdAttr)).collect(toList());
            String indexFieldName = getQueryFieldName(refAttributePath);
            return QueryBuilders.boolQuery().mustNot(QueryBuilders.nestedQuery(fieldName, QueryBuilders.existsQuery(indexFieldName), ScoreMode.Avg));
        case COMPOUND:
            throw new MolgenisQueryException(format("Illegal attribute type [%s]", attrType.toString()));
        default:
            throw new UnexpectedEnumException(attrType);
    }
}