Examples with EntryLinks org.jbei.ice.lib.entry.EntryLinks used on opensource projects

Example 1 with EntryLinks

use of org.jbei.ice.lib.entry.EntryLinks in project ice by JBEI.

the class SBOLParser method createICEComponentDefinitionRecord.

protected void createICEComponentDefinitionRecord(SBOLDocument document, ComponentDefinition componentDefinition) throws SBOLValidationException {
    SBOLDocument rootedDocument = document.createRecursiveCopy(componentDefinition);
    String identity = componentDefinition.getIdentity().toString();
    Long partId = identityEntryMap.get(identity);
    if (partId == null) {
        createNewEntry(componentDefinition, rootedDocument);
    }
    // Add rootedDocument as the SBOL associated with this record
    for (Component component : componentDefinition.getComponents()) {
        if (component.getDefinition() == null)
            continue;
        Long componentId = identityEntryMap.get(component.getDefinition().getIdentity().toString());
        if (componentId == null) {
            SBOLDocument sbolDocument = document.createRecursiveCopy(component.getDefinition());
            componentId = createNewEntry(component.getDefinition(), sbolDocument);
        }
        EntryLinks links = new EntryLinks(userId, componentId.toString());
        links.addLink(this.partData, LinkType.PARENT);
        Logger.debug("    Link to ComponentDefinition: " + component.getDefinition().getIdentity());
    }
}

Example 2 with EntryLinks

use of org.jbei.ice.lib.entry.EntryLinks in project ice by JBEI.

the class BulkUploadEntries method doUpdate.

private PartData doUpdate(String userId, Entry entry, PartData data) {
    if (entry == null)
        return null;
    Entries entries = new Entries(userId);
    entries.update(entry.getId(), data);
    // check if there is any linked parts. update if so (expect a max of 1)
    if (data.getLinkedParts() == null || data.getLinkedParts().isEmpty())
        return data;
    // retrieve the entry (this is the only time you can create another entry on update)
    // bulk upload can only link 1
    PartData linkedPartData = data.getLinkedParts().get(0);
    Entry linkedEntry = entryDAO.get(linkedPartData.getId());
    if (linkedEntry == null && !StringUtils.isEmpty(linkedPartData.getPartId())) {
        // try partId
        linkedEntry = entryDAO.getByPartNumber(linkedPartData.getPartId());
        if (linkedEntry != null)
            linkedPartData.setId(linkedEntry.getId());
    }
    if (linkedEntry == null) {
        // create new object for linked entry
        linkedEntry = InfoToModelFactory.infoToEntry(linkedPartData);
        if (linkedEntry != null) {
            linkedEntry.setVisibility(Visibility.DRAFT.getValue());
            Account account = accountController.getByEmail(userId);
            linkedEntry.setOwner(account.getFullName());
            linkedEntry.setOwnerEmail(account.getEmail());
            linkedEntry = entryDAO.create(linkedEntry);
            entry.getLinkedEntries().add(linkedEntry);
            entryDAO.update(linkedEntry);
            linkedPartData.setId(linkedEntry.getId());
        }
    } else {
        // linking to existing
        EntryLinks entryLinks = new EntryLinks(userId, Long.toString(entry.getId()));
        entryLinks.addLink(linkedPartData, LinkType.CHILD);
    }
    // recursively update
    PartData linked = doUpdate(userId, linkedEntry, linkedPartData);
    data.getLinkedParts().clear();
    if (linked != null)
        data.getLinkedParts().add(linked);
    return data;
}

Example 3 with EntryLinks

use of org.jbei.ice.lib.entry.EntryLinks in project ice by JBEI.

the class SBOLParser method createICEModuleDefinitionRecord.

protected void createICEModuleDefinitionRecord(SBOLDocument document, ModuleDefinition moduleDefinition) throws SBOLValidationException {
    SBOLDocument rootedDocument = document.createRecursiveCopy(moduleDefinition);
    Logger.debug("Creating ICE record for ModuleDefinition: " + moduleDefinition.getIdentity());
    String identity = moduleDefinition.getIdentity().toString();
    Long partId = identityEntryMap.get(identity);
    if (partId == null) {
        Logger.debug("Creating " + moduleDefinition.getDisplayId());
        createNewEntry(moduleDefinition, rootedDocument);
    }
    for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
        ComponentDefinition componentDefinition = functionalComponent.getDefinition();
        // Note: record may not exist yet, so you might need to create it now too
        if (componentDefinition == null)
            continue;
        Long componentId = identityEntryMap.get(componentDefinition.getIdentity().toString());
        if (componentId == null) {
            SBOLDocument sbolDocument = document.createRecursiveCopy(componentDefinition);
            componentId = createNewEntry(componentDefinition, sbolDocument);
        }
        EntryLinks links = new EntryLinks(userId, componentId.toString());
        links.addLink(this.partData, LinkType.PARENT);
    }
    // Note: record may not exist yet, so you might need to create it now too
    for (Module module : moduleDefinition.getModules()) {
        if (module.getDefinition() == null)
            continue;
        Long moduleId = identityEntryMap.get(module.getDefinition().getIdentity().toString());
        if (moduleId == null) {
            SBOLDocument moduleDocument = document.createRecursiveCopy(module.getDefinition());
            moduleId = createNewEntry(module.getDefinition(), moduleDocument);
        }
        EntryLinks links = new EntryLinks(userId, moduleId.toString());
        links.addLink(this.partData, LinkType.PARENT);
        Logger.debug("    Link to ModuleDefinition: " + module.getDefinition().getIdentity());
    }
}