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

Example 36 with PartData

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

the class EntryLinks method get.

/**
     * Retrieves entry links that are parents or children depending on specified type
     *
     * @param type specified type of links to return
     * @return list of links that match specified type. These are filtered based on user permissions
     */
public List<PartData> get(LinkType type) {
    List<Entry> entries;
    if (type == LinkType.CHILD) {
        entries = new ArrayList<>(this.entry.getLinkedEntries());
    } else {
        entries = this.entryDAO.getParents(this.entry.getId());
    }
    // get sequence and other summary information
    List<PartData> results = new ArrayList<>(entries.size());
    for (Entry entry : entries) {
        if (!this.entryAuthorization.canRead(this.userId, entry))
            continue;
        PartData partData = new PartData(EntryType.nameToType(entry.getRecordType()));
        partData.setId(entry.getId());
        partData.setName(entry.getName());
        partData.setPartId(entry.getPartNumber());
        partData.setShortDescription(entry.getShortDescription());
        boolean hasSequence = sequenceDAO.hasSequence(entry.getId());
        partData.setHasSequence(hasSequence);
        boolean hasOriginalSequence = sequenceDAO.hasOriginalSequence(entry.getId());
        partData.setHasOriginalSequence(hasOriginalSequence);
        Optional<String> sequenceString = sequenceDAO.getSequenceString(entry);
        if (sequenceString.isPresent()) {
            String sequence = sequenceString.get();
            int featureCount = sequenceFeatureDAO.getFeatureCount(entry);
            partData.setBasePairCount(sequence.trim().length());
            partData.setFeatureCount(featureCount);
        } else {
            partData.setBasePairCount(0);
        }
        results.add(partData);
    }
    return results;
}

Example 37 with PartData

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

the class FolderContents method addToRemoteFolder.

// transfer entries to remote partner and add to folder
protected void addToRemoteFolder(Account account, Folder folder, List<Long> entries) {
    RemoteAccessModel remoteAccessModel = remoteAccessModelDAO.getByFolder(account, folder);
    if (remoteAccessModel == null) {
        Logger.error("Could not retrieve remote access for folder " + folder.getId());
        return;
    }
    RemotePartner remotePartner = remoteAccessModel.getRemoteClientModel().getRemotePartner();
    RemoteTransfer remoteTransfer = new RemoteTransfer();
    List<PartData> results = remoteTransfer.getPartsForTransfer(entries);
    List<Long> remoteIds = remoteTransfer.transferEntries(remotePartner.getId(), results);
    FolderDetails remoteFolder = new FolderDetails();
    remoteFolder.setId(Long.decode(remoteAccessModel.getIdentifier()));
    // add transferred entries to the folder
    EntrySelection selection = new EntrySelection();
    selection.getEntries().addAll(remoteIds);
    selection.getDestination().add(remoteFolder);
    selection.setSelectionType(EntrySelectionType.FOLDER);
    String token = remoteAccessModel.getToken();
    remoteContact.addTransferredEntriesToFolder(remotePartner.getUrl(), account.getEmail(), selection, remoteFolder.getId(), token, remotePartner.getApiKey());
}

Example 38 with PartData

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

the class Strain method toDataTransferObject.

@Override
public PartData toDataTransferObject() {
    PartData data = super.toDataTransferObject();
    StrainData strainData = new StrainData();
    strainData.setGenotypePhenotype(genotypePhenotype);
    strainData.setHost(host);
    data.setStrainData(strainData);
    return data;
}

Example 39 with PartData

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

the class Request method toDataTransferObject.

@Override
public SampleRequest toDataTransferObject() {
    SampleRequest sampleRequest = new SampleRequest();
    sampleRequest.setId(getId());
    sampleRequest.setRequestType(getType());
    sampleRequest.setStatus(getStatus());
    if (growthTemperature != null)
        sampleRequest.setGrowthTemperature(growthTemperature);
    sampleRequest.setPlateDescription(plateDescription);
    EntryType type = EntryType.nameToType(entry.getRecordType());
    PartData data = new PartData(type);
    data.setId(entry.getId());
    data.setPartId(entry.getPartNumber());
    data.setSelectionMarkers(EntryUtil.getSelectionMarkersAsList(entry.getSelectionMarkers()));
    data.setName(entry.getName());
    sampleRequest.setPartData(data);
    sampleRequest.setRequester(getAccount().toDataTransferObject());
    sampleRequest.setRequestTime(getRequested().getTime());
    sampleRequest.setUpdateTime(getUpdated() == null ? sampleRequest.getRequestTime() : getUpdated().getTime());
    return sampleRequest;
}

Example 40 with PartData

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

the class FolderContentsTest method testGetContents.

@Test
public void testGetContents() throws Exception {
    FolderContents folderContents = new FolderContents();
    // test with null id
    folderContents.getContents(null, 0, new PageParameters(0, 10, ColumnField.PART_ID, false, null));
    Account account = AccountCreator.createTestAccount("testRetrieveFolderContents", false);
    String userId = account.getEmail();
    FolderDetails folderDetails = new FolderDetails();
    folderDetails.setName("test");
    // create folder
    FolderDetails folder = createPersonalFolder(userId, folderDetails);
    Assert.assertNotNull(folder);
    final short size = 105;
    // create 100 test strains
    HashMap<String, Entry> parts = new HashMap<>();
    List<Long> entryList = new ArrayList<>();
    for (int i = 0; i < size; i += 1) {
        Strain strain = TestEntryCreator.createTestStrain(account);
        Assert.assertNotNull(strain);
        parts.put(strain.getPartNumber(), strain);
        entryList.add(strain.getId());
    }
    Assert.assertEquals(size, parts.size());
    // add to folder
    List<FolderDetails> foldersToAdd = new ArrayList<>();
    foldersToAdd.add(folder);
    foldersToAdd = folderContents.addEntriesToFolders(account.getEmail(), entryList, foldersToAdd);
    Assert.assertNotNull(foldersToAdd);
    // keep track to find duplicates
    HashSet<Long> set = new HashSet<>();
    // retrieve (supported sort types created, status, name, part_id, type)
    FolderDetails details = folderContents.getContents(account.getEmail(), folder.getId(), new PageParameters(0, 15, ColumnField.PART_ID, false, null));
    Assert.assertNotNull(details);
    short pageSize = 15;
    int it = 1;
    while (!details.getEntries().isEmpty()) {
        Assert.assertEquals(pageSize, details.getEntries().size());
        for (PartData partData : details.getEntries()) {
            Assert.assertNotNull(parts.remove(partData.getPartId()));
            Assert.assertFalse(set.contains(partData.getId()));
            set.add(partData.getId());
        }
        // check remaining
        Assert.assertEquals((size - (it * pageSize)), parts.size());
        details = folderContents.getContents(account.getEmail(), folder.getId(), new PageParameters(pageSize * it, pageSize, ColumnField.PART_ID, false, null));
        it += 1;
    }
}