private static void transformRefEntity( Attribute attribute, Map<String, EntityType> newEntityTypes) { if (attribute.getRefEntity() != null) { String refId = attribute.getRefEntity().getId(); if (newEntityTypes.containsKey(refId)) { attribute.setRefEntity(newEntityTypes.get(refId)); } } }
@Override public List<Attribute> getRequiredAttributes() { List<Attribute> requiredAttributes = new ArrayList<>(); EntityType entityType = entityTypeFactory.create(VARIANT); List<Attribute> refAttributesList = Arrays.asList(createCaddScaledAttr(attributeFactory), getExacAFAttr(attributeFactory), vcfAttributes.getAltAttribute()); entityType.addAttributes(refAttributesList); Attribute refAttr = attributeFactory.create() .setName(VARIANT) .setDataType(XREF) .setRefEntity(entityType) .setDescription( "This annotator needs a references to an entity containing: " + StreamSupport.stream( refAttributesList.spliterator(), false) .map(Attribute::getName) .collect(Collectors.joining(", "))); requiredAttributes.addAll( Arrays.asList(effectsMetaData.getGeneNameAttr(), effectsMetaData.getPutativeImpactAttr(), refAttr, effectsMetaData.getAltAttr())); return requiredAttributes; }
@Override public void init() { setLabel("Mapping project"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(NAME).setNillable(false); addAttribute(OWNER).setDataType(XREF).setRefEntity(userMetaData); addAttribute(MAPPING_TARGETS).setDataType(MREF).setRefEntity(mappingTargetMetaData).setCascadeDelete(true); } }
private void createResultEntityType(Entity effect, EntityType variantEMD) { if (vcfVariantEntityType == null || effectEntityType == null) { effectEntityType = effect.getEntityType(); vcfVariantEntityType = EntityType.newInstance(variantEMD); vcfVariantEntityType.addAttribute( attributeFactory.create().setName(EFFECT).setDataType(MREF).setRefEntity(effectEntityType)); } }
private void createResultEntityType(Entity effect, EntityType variantEMD) { if (vcfVariantEntityType == null || effectEntityType == null) { effectEntityType = effect.getEntityType(); vcfVariantEntityType = EntityType.newInstance(variantEMD); vcfVariantEntityType.addAttribute( attributeFactory.create().setName(EFFECT).setDataType(MREF).setRefEntity(effectEntityType)); } }
@Override public void init() { setLabel("Entity mapping"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(SOURCE_ENTITY_TYPE); addAttribute(TARGET_ENTITY_TYPE); addAttribute(ATTRIBUTE_MAPPINGS).setDataType(MREF).setRefEntity(attributeMappingMetaData) .setCascadeDelete(true); } }
@Override protected void init() { setLabel(SIMPLE_NAME); setPackage(settingsPackage); addAttribute(ID, ROLE_ID).setAuto(true).setVisible(false); addAttribute(NAME, ROLE_LABEL).setNillable(false).setDataType(STRING); addAttribute(BOOTSTRAP_3_THEME) .setNillable(false) .setDataType(FILE) .setRefEntity(fileMetaMetaData); addAttribute(BOOTSTRAP_4_THEME) .setNillable(true) .setDataType(FILE) .setRefEntity(fileMetaMetaData); } }
@Override public void init() { setLabel("Mapping target"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(ENTITY_MAPPINGS).setDataType(MREF).setRefEntity(entityMappingMetaData).setCascadeDelete(true); addAttribute(TARGET).setNillable(false); } }
@Override public void init() { setLabel("Mapping target"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(ENTITY_MAPPINGS) .setDataType(MREF) .setRefEntity(entityMappingMetaData) .setCascadeDelete(true); addAttribute(TARGET).setNillable(false); } }
@Override public void init() { setLabel("Entity mapping"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(SOURCE_ENTITY_TYPE); addAttribute(TARGET_ENTITY_TYPE); addAttribute(ATTRIBUTE_MAPPINGS) .setDataType(MREF) .setRefEntity(attributeMappingMetaData) .setCascadeDelete(true); } }
@Override public void init() { setLabel("Ontology term"); setPackage(ontologyPackage); addAttribute(ID, ROLE_ID).setVisible(false); addAttribute(ONTOLOGY_TERM_IRI).setNillable(false); addAttribute(ONTOLOGY_TERM_NAME, ROLE_LABEL).setDataType(TEXT).setNillable(false); addAttribute(ONTOLOGY_TERM_SYNONYM) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermSynonymMetaData) .setCascadeDelete(true); addAttribute(ONTOLOGY_TERM_DYNAMIC_ANNOTATION) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermDynamicAnnotationMetaData) .setCascadeDelete(true); addAttribute(ONTOLOGY_TERM_NODE_PATH) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermNodePathMetaData) .setCascadeDelete(true); addAttribute(ONTOLOGY).setDataType(XREF).setNillable(false).setRefEntity(ontologyMetaData); } }
@Override public void init() { setLabel("Ontology term hit"); setPackage(ontologyPackage); addAttribute(ID, ROLE_ID).setAuto(true); addAttribute(SCORE).setDataType(DECIMAL); addAttribute(COMBINED_SCORE).setDataType(DECIMAL); // Append OntologyTermMetaData attributes with the same name (required by SORTA) addAttribute(ONTOLOGY_TERM_IRI).setNillable(false); addAttribute(ONTOLOGY_TERM_NAME, ROLE_LABEL).setDataType(TEXT).setNillable(false); addAttribute(ONTOLOGY_TERM_SYNONYM) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermSynonymMetaData); addAttribute(ONTOLOGY_TERM_DYNAMIC_ANNOTATION) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermDynamicAnnotationMetaData); addAttribute(ONTOLOGY_TERM_NODE_PATH) .setDataType(MREF) .setNillable(true) .setRefEntity(ontologyTermNodePathMetaData); addAttribute(ONTOLOGY).setDataType(XREF).setNillable(false).setRefEntity(ontologyMetaData); } }
@Override public void init() { setLabel("Mapping project"); setPackage(mapperPackage); addAttribute(IDENTIFIER, ROLE_ID); addAttribute(NAME).setNillable(false); addAttribute(DEPTH).setDataType(INT).setRangeMin(1L); addAttribute(MAPPING_TARGETS) .setDataType(MREF) .setRefEntity(mappingTargetMetaData) .setCascadeDelete(true); } }
@Override public void init() { setLabel("Mail sender properties"); setDescription( "See https://javamail.java.net/nonav/docs/api/ for a description of the properties you can use."); setPackage(mailPackage); setExtends(propertyType); addAttribute(MAIL_SETTINGS_REF) .setDataType(XREF) .setRefEntity(mailSettings) .setLabel("MailSettings") .setDescription( "Reference to the (unique) MailSettings entity that these properties belong to.") .setVisible(false) .setNillable(false) .setReadOnly(true); } }
private void createEmptyResultRepository( String jobName, String resultEntityName, EntityType sourceMetaData) { EntityType resultEntityType = EntityType.newInstance(matchingTaskContentMetaData, DEEP_COPY_ATTRS, attrMetaFactory); resultEntityType.setId(resultEntityName); resultEntityType.setPackage(null); resultEntityType.setAbstract(false); resultEntityType.addAttribute( attrMetaFactory .create() .setName(INPUT_TERM) .setDataType(XREF) .setRefEntity(sourceMetaData) .setDescription("Reference to the input term") .setNillable(false)); resultEntityType.setLabel(jobName + " output"); dataService.getMeta().addEntityType(resultEntityType); }
.setDescription("OpenID Connect client") .setDataType(XREF) .setRefEntity(oidcClientMetadata) .setNillable(false); addAttribute(OIDC_USERNAME) .setDescription("MOLGENIS user") .setDataType(XREF) .setRefEntity(userMetaData) .setNillable(false);
@Override public void init() { setLabel(SIMPLE_NAME); setPackage(ontologyPackage); addAttribute(ID, ROLE_ID).setVisible(false); addAttribute(ONTOLOGY_IRI) .setNillable(false) .setLabel("IRI") .setDescription("IRI which is used to identify an ontology"); addAttribute(ONTOLOGY_NAME, ROLE_LABEL).setNillable(false).setLabel("Name"); addAttribute(ONTOLOGY_TERMS) .setDataType(ONE_TO_MANY) .setRefEntity(ontologyTermMetaData) .setMappedBy(ontologyTermMetaData.getAttribute(OntologyTermMetaData.ONTOLOGY)) .setCascadeDelete(true) .setLabel("Terms"); }
@Override public void init() { setLabel("Scheduled Job Type"); setPackage(jobPackage); addAttribute(NAME, ROLE_ID).setLabel("Name"); addAttribute(LABEL, ROLE_LABEL).setDataType(STRING).setLabel("Label"); addAttribute(DESCRIPTION).setDataType(TEXT).setLabel("Description").setNillable(true); addAttribute(JOB_EXECUTION_TYPE) .setDataType(XREF) .setRefEntity(entityTypeMetadata) .setNillable(false); addAttribute(SCHEMA) .setDataType(TEXT) .setLabel("JSON Schema for the job parameters") .setNillable(true); } }
@Override public void init() { setLabel("File ingest job execution"); setExtends(jobExecutionMetaData); setPackage(jobPackage); addAttribute(FILE) .setLabel("File") .setDescription("The imported file.") .setDataType(XREF) .setRefEntity(fileMetaMetaData) .setNillable(true); addAttribute(URL) .setLabel("Url") .setDescription("Url of the file to download.") .setNillable(false); addAttribute(LOADER) .setDataType(ENUM) .setEnumOptions(LOADERS) .setLabel("Loader type") .setNillable(false); addAttribute(TARGET_ENTITY_ID) .setDataType(STRING) .setLabel("Target EntityType ID") .setNillable(false); } }
@Override public void init() { setLabel("Index action"); setPackage(indexPackage); addAttribute(ID, ROLE_ID).setAuto(true).setVisible(false); addAttribute(CREATION_DATE_TIME, ROLE_LABEL).setDataType(AttributeType.DATE_TIME).setAuto(true); addAttribute(INDEX_ACTION_GROUP_ATTR) .setDescription("The group that this index action belongs to") .setDataType(XREF) .setRefEntity(indexActionGroupMetaData); addAttribute(ACTION_ORDER) .setDataType(INT) .setDescription("The order in which the action is registered within its IndexActionJob") .setNillable(false); addAttribute(ENTITY_TYPE_ID) .setDescription("The id of the entity type that needs to be indexed (e.g. myEntityType).") .setNillable(false); addAttribute(ENTITY_ID) .setDescription("The id of the entity that needs to be indexed") .setDataType(TEXT) .setNillable(true); addAttribute(INDEX_STATUS) .setDescription("The status of index action") .setDataType(ENUM) .setEnumOptions(IndexStatus.class) .setNillable(false); }