/core2/src/main/java/org/synbiohub/frontend/SynBioHubFrontend.java

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package org.synbiohub.frontend;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URI;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;

import org.apache.commons.io.IOUtils;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.NameValuePair;
import org.apache.http.client.HttpClient;
import org.apache.http.client.config.RequestConfig;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpRequestBase;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.mime.HttpMultipartMode;
import org.apache.http.entity.mime.MultipartEntityBuilder;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.client.HttpClients;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.apache.http.message.BasicNameValuePair;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.sbolstandard.core2.SBOLDocument;
import org.sbolstandard.core2.SBOLReader;
import org.sbolstandard.core2.SBOLValidationException;
import org.sbolstandard.core2.SBOLWriter;
import org.sbolstandard.core2.TopLevel;

import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;

/**
 * Provides a Java API to SynBioHub instances.
 * @author James McLaughlin
 * @author Chris Myers
 *
 */
public class SynBioHubFrontend
{
    PoolingHttpClientConnectionManager connectionManager;
    HttpClient client;
    String backendUrl;
    String uriPrefix;
    String user = "";
    String username = null;

    /**
     * Creates an instance of the SynBioHub API.
     * @param backendUrl - URL for the SynBioHub instance.
     * @param uriPrefix - prefix for all URIs stored in this repository
     */
    public SynBioHubFrontend(String backendUrl, String uriPrefix)
    {
        this.backendUrl = backendUrl;
        this.uriPrefix = uriPrefix;

        connectionManager = new PoolingHttpClientConnectionManager();
        client = HttpClients.custom().setConnectionManager(connectionManager).build();
    }

    /**
     * Creates an instance of the SynBioHub API.
     * @param backendUrl - URL for the SynBioHub instance.
     */
    public SynBioHubFrontend(String backendUrl)
    {
        this.backendUrl = backendUrl;
        this.uriPrefix = backendUrl;

        connectionManager = new PoolingHttpClientConnectionManager();
        client = HttpClients.custom().setConnectionManager(connectionManager).build();
    }
    
    /**
     * Creates an instance of the SynBioHub API.
     * @param backendUrl - URL for the SynBioHub instance.
     * @param timeout - timeout for connections in seconds
     */
    public SynBioHubFrontend(String backendUrl,int timeout)
    {
        this.backendUrl = backendUrl;
        this.uriPrefix = backendUrl;

        connectionManager = new PoolingHttpClientConnectionManager();
//        client = HttpClients.custom().setConnectionManager(connectionManager).build();
    	RequestConfig config = RequestConfig.custom()
    			.setConnectTimeout(timeout * 1000)
    			.setConnectionRequestTimeout(timeout * 1000)
    			.setSocketTimeout(timeout * 1000).build();
    	client = HttpClientBuilder.create().setDefaultRequestConfig(config).build();
    }

    /**
     * Creates an instance of the SynBioHub API.
     * @param backendUrl - URL for the SynBioHub instance.
     * @param uriPrefix - prefix for all URIs stored in this repository
     * @param timeout - timeout for connections in seconds
     */
    public SynBioHubFrontend(String backendUrl, String uriPrefix, int timeout)
    {
        this.backendUrl = backendUrl;
        this.uriPrefix = uriPrefix;

        connectionManager = new PoolingHttpClientConnectionManager();

        RequestConfig config = RequestConfig.custom()
                .setConnectTimeout(timeout * 1000)
                .setConnectionRequestTimeout(timeout * 1000)
                .setSocketTimeout(timeout * 1000).build();
        client = HttpClientBuilder.create().setDefaultRequestConfig(config).build();
    }


    /**
     * Returns the URL for the SynBioHub instance.
     * @return the URL for the SynBioHub instance.
     */
    public String getBackendUrl()
    {
        return this.backendUrl;
    }

    /**
     * Return the total number of objects of a specified type in the repository.
     *
     * @return the total number of objects of a specified type in the repository.
     *
     * @param objectType The object type to count 
     * (Collection, ComponentDefinition, Sequence, ModuleDefinition, Model, etc.).
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */ 
    public int getCount(String objectType) throws SynBioHubException
    {
        return fetchCount(backendUrl + "/" + objectType + "/count");
    }
    
    /**
     * Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
     *
     * @param topLevelUri The URI of the SBOL TopLevel
     *
     * @return A libSBOLj TopLevel instance corresponding to the TopLevel
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public SBOLDocument getSBOL(URI topLevelUri) throws SynBioHubException
    {
         return getSBOL(topLevelUri,true);
    }
    
    /**
     * Retrieve SBOL TopLevel object from a SynBioHub instance using its URI.
     *
     * @param topLevelUri The URI of the SBOL TopLevel
     * @param recursive indicates if the complete SBOL document should be fetched recursively
     *
     * @return A libSBOLj TopLevel instance corresponding to the TopLevel
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public SBOLDocument getSBOL(URI topLevelUri,boolean recursive) throws SynBioHubException
    {
    	if (topLevelUri==null) return null;
        if (!topLevelUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelUri + "/sbol";
        if (!recursive) {
        	url = topLevelUri + "/sbolnr";
        }
        url = url.replace(uriPrefix, backendUrl);

        try {
        	SBOLDocument document = fetchFromSynBioHub(url);
        	return document;
        } catch (NotFoundException e) {
        	return null;
        }
    }
    
    /**
     * Retrieve a GFF3 version of a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getGFF3(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/gff";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve a GFF3 version of a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getGFF3(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/gff";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Retrieve a GenBank version of a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getGenBank(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/gb";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve a GenBank version of a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getGenBank(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/gb";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Retrieve a FASTA version of a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getFASTA(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/fasta";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve a GenBank version of a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getFASTA(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/fasta";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Retrieve a JSON version of a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getJSON(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/summary";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve a JSON version of a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getJSON(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/summary";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Retrieve metadata for a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getMetadata(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/metadata";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve metadata for a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getMetadata(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/metadata";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Retrieve a COMBINE Archive version of a topLevel object from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getArchive(URI topLevelURI, String path) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/omex";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve a COMBINE Archive version of a topLevel object from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param topLevelURI The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getArchive(URI topLevelURI, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!topLevelURI.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelURI + "/omex";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
        
    /**
     * Retrieve an attachment from a SynBioHub instance using its URI,
     * and save to the path provided.
     *
     * @param attachmentUri The URI of the SBOL Attachment object
     * @param path The path to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getAttachment(URI attachmentUri, String path) throws SynBioHubException, IOException
    {
        if (!attachmentUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = attachmentUri + "/download";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,null,path);
    }
    
    /**
     * Retrieve an attachment from a SynBioHub instance using its URI,
     * and save into the provided output stream.
     *
     * @param attachmentUri The URI of the SBOL Attachment object
     * @param outputStream The output stream to store the downloaded attachment
     * @return the name of the file being downloaded
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     * @throws IOException if there is an I/O error
     */
    public String getAttachment(URI attachmentUri, OutputStream outputStream) throws SynBioHubException, IOException
    {
        if (!attachmentUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = attachmentUri + "/download";
        url = url.replace(uriPrefix, backendUrl);

        return fetchContentSaveToFile(url,outputStream,null);
    }
    
    /**
     * Remove SBOL Collection from a SynBioHub instance using its URI.
     *
     * @param topLevelUri The URI of the SBOL Collection
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void removeCollection(URI topLevelUri) throws SynBioHubException
    {
        if (!topLevelUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelUri + "/removeCollection";
        url = url.replace(uriPrefix, backendUrl);

        removeFromSynBioHub(url);
    }
    
    /**
     * Remove SBOL TopLevel object from a SynBioHub instance using its URI.
     *
     * @param topLevelUri The URI of the SBOL TopLevel
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void removeSBOL(URI topLevelUri) throws SynBioHubException
    {
        if (!topLevelUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelUri + "/remove";
        url = url.replace(uriPrefix, backendUrl);

        removeFromSynBioHub(url);
    }
    
    /**
     * Remove SBOL TopLevel object from a SynBioHub instance using its URI,
     * but leave references to this object, since it is going to be replaced.
     *
     * @param topLevelUri The URI of the SBOL TopLevel
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void replaceSBOL(URI topLevelUri) throws SynBioHubException
    {
        if (!topLevelUri.toString().startsWith(uriPrefix)) {
        	throw new SynBioHubException("Object URI does not start with correct URI prefix for this repository.");
        }
        String url = topLevelUri + "/replace";
        url = url.replace(uriPrefix, backendUrl);

        removeFromSynBioHub(url);
    }

   /**
     * Search the default store for ComponentDefinition instances matching a name and/or a set of roles
     *
     * @param name The dcterms:title to search for, or null
     * @param roles A set of role URIs to search for, or null
     * @param types A set of type URIs to search for, or null
     * @param collections A set of Collection URIs to search for, or null
     * @param offset The offset of the results to begin at, or null to begin at 0
     * @param limit The maximum number of results to return, or null to return all results
     *
     * @return An ArrayList of ComponentDefinitionMetaData objects with a summary of all matching ComponentDefinitions.
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public ArrayList<IdentifiedMetadata> getMatchingComponentDefinitionMetadata(String name, Set<URI> roles, 
    		Set<URI> types, Set<URI> collections, Integer offset, Integer limit)
            throws SynBioHubException
    {
    	SearchQuery query = new SearchQuery();

    	query.setOffset(offset);
    	query.setLimit(limit);

    	SearchCriteria objectCriteria = new SearchCriteria();
    	objectCriteria.setKey("objectType");
    	objectCriteria.setValue("ComponentDefinition");
    	query.addCriteria(objectCriteria);
    	if (roles != null) {
    		for(URI uri : roles)
    		{
    			SearchCriteria roleCriteria = new SearchCriteria();

    			roleCriteria.setKey("role");
    			roleCriteria.setValue(uri.toString());

    			query.getCriteria().add(roleCriteria);
        	}	
        }
        
        if (types != null) {
        	for(URI uri : types)
        	{
        		SearchCriteria typeCriteria = new SearchCriteria();

        		typeCriteria.setKey("type");
        		typeCriteria.setValue(uri.toString());

        		query.getCriteria().add(typeCriteria);
        	}
        }
        
        if (collections != null) {
        	for(URI uri : collections)
        	{
        		SearchCriteria collectionCriteria = new SearchCriteria();

        		collectionCriteria.setKey("collection");
        		collectionCriteria.setValue(uri.toString());

        		query.getCriteria().add(collectionCriteria);
        	}
        }

        if(name != null)
        {
            SearchCriteria nameCriteria = new SearchCriteria();

            nameCriteria.setKey("name");
            nameCriteria.setValue(name);

            query.getCriteria().add(nameCriteria);
        }
    	return search(query);
    }
    
    private String constructQueryURL(String url,SearchQuery query) {
        //query.offset = offset;
        //query.limit = limit;

        String textQuery = "";
        boolean first = true;
        for (SearchCriteria criteria : query.getCriteria()) {
        	if (criteria.getKey().equals("objectType")) {
        		url += encodeUri(criteria.getKey()+"="+criteria.getValue()+"&");
        		continue;
        	}
        	if (criteria.getKey().equals("name")) {
        		if (first) first = false;
        		else textQuery = " ";
        		textQuery = criteria.getValue();
        		continue;
        	} 
        	if (criteria.getKey().startsWith("http")) {
        		url += encodeUri("<" + criteria.getKey() + ">=");
        	} else {
        		url += encodeUri(criteria.getKey()+"=");
        	}
        	if (criteria.getValue().startsWith("http")) {
        		url += encodeUri("<"+criteria.getValue()+">&");
        	} else {
        		url += encodeUri("'"+criteria.getValue()+"'&");
        	}
        }
        url += encodeUri(textQuery);
        if (query.getOffset()!=null && query.getLimit()!=null) {
        	url += "/?offset="+query.getOffset() + "&" + "limit="+query.getLimit();
        } else if (query.getOffset()!=null) {
        	url += "/?offset="+query.getOffset();
        } else if (query.getLimit()!=null) {
        	url += "/?limit="+query.getLimit();
        }
        
    	return url;
    }
    
    /**
     * Search this SynBioHub instance for objects matching a search query
     * 
     * @param query the search query
     *
     * @return An ArrayList of MetaData for objects that match the specified search query
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public ArrayList<IdentifiedMetadata> search(SearchQuery query) throws SynBioHubException
    {
        String url = backendUrl + "/search/";

        //query.offset = offset;
        //query.limit = limit;

        url = constructQueryURL(url,query);
 
       	//System.out.println(url);
        Gson gson = new Gson();

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            ArrayList<IdentifiedMetadata> metadataList = gson.fromJson(
            		new InputStreamReader(inputStream),
            			new TypeToken<ArrayList<IdentifiedMetadata>>(){}.getType());
            
            return metadataList;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Search this SynBioHub instance for objects matching a search query
     * and return the number of matches
     * 
     * @param query the search query
     *
     * @return the number of objects matching a search query
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public int searchCount(SearchQuery query) throws SynBioHubException
    {
        String url = backendUrl + "/searchCount/";

        //query.offset = offset;
        //query.limit = limit;

        url = constructQueryURL(url,query);
        return fetchCount(url);
    }
    
    /**
     * Search the default store for Collections that are not members of any other Collections
     *
     * @return An ArrayList of CollectionMetaData objects with a summary of all matching Collections.
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public ArrayList<IdentifiedMetadata> getRootCollectionMetadata()
            throws SynBioHubException
    {
        String url = backendUrl + "/rootCollections";

        Gson gson = new Gson();

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            ArrayList<IdentifiedMetadata> metadataList = gson.fromJson(
            		new InputStreamReader(inputStream),
            			new TypeToken<ArrayList<IdentifiedMetadata>>(){}.getType());
            
            return metadataList;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Search the default store for submissions from the specified user
     *
     * @return An ArrayList of MetaData for all submissions for the specified user.
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public ArrayList<IdentifiedMetadata> getSubmissionsMetadata()
            throws SynBioHubException
    {
        String url = backendUrl + "/manage";

        Gson gson = new Gson();

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            ArrayList<IdentifiedMetadata> metadataList = gson.fromJson(
            		new InputStreamReader(inputStream),
            			new TypeToken<ArrayList<IdentifiedMetadata>>(){}.getType());
            
            return metadataList;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Search the default store for objects that are shared with the specified user
     *
     * @return An ArrayList of MetaData for all shared objects.
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public ArrayList<IdentifiedMetadata> getSharedMetadata()
            throws SynBioHubException
    {
        String url = backendUrl + "/shared";

        Gson gson = new Gson();

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            ArrayList<IdentifiedMetadata> metadataList = gson.fromJson(
            		new InputStreamReader(inputStream),
            			new TypeToken<ArrayList<IdentifiedMetadata>>(){}.getType());
            
            return metadataList;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Get configuration of a SynBioHub
     *
     * @return A JSON object of the configuration of a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONObject getConfig() throws SynBioHubException
    {
    	return getConfig("");
    }
    
    /**
     * Get graphs in a SynBioHub
     *
     * @return A JSON array of the graphs in a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONArray getGraphs() throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to get the graphs.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/graphs";

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            JSONParser parser = new JSONParser();
            JSONArray config = (JSONArray) parser.parse(inputStreamToString(inputStream));
            
            return config;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Get graphs in a SynBioHub
     *
     * @return A JSONObject of the graphs in a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONArray getLogs() throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to get the logs.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/log";

        HttpGet request = new HttpGet(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");

        try
        {
            HttpResponse response = client.execute(request);

            checkResponseCode(response);

            InputStream inputStream = response.getEntity().getContent();

            JSONParser parser = new JSONParser();
            JSONArray config = (JSONArray) parser.parse(inputStreamToString(inputStream));
            
            return config;
        }
        catch (Exception e)
        {
            throw new SynBioHubException(e);
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Get mail configuration of a SynBioHub
     *
     * @return A JSON object of the mail configuration of a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONObject getMailConfig() throws SynBioHubException
    {
    	return getConfig("mail");
    }
    
    /**
     * Set the mail configuration for a SynBioHub
     * 
     * @param key SendGrid API Key
     * @param fromEmail SendGrid from Email
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void setMailConfig(String key, String fromEmail) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to set the mail configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/mail";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("key", key));
        arguments.add(new BasicNameValuePair("fromEmail", fromEmail));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }   
    
    /**
     * Get plugin configuration for a SynBioHub
     *
     * @return A JSON object of the plugin configuration for a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONObject getPluginsConfig() throws SynBioHubException
    {
    	return getConfig("plugins");
    }
    
    /**
     * Edit a plugin configuration in a SynBioHub
     * 
     * @param id Id of plugin
     * @param category Type of plugin (rendering, submit, download)
     * @param name Name of the plugin
     * @param pluginURL URL for the plugin
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void editPluginConfig(int id, String category, String name, String pluginURL) throws SynBioHubException
    {
        id = id + 1;
    	savePluginConfig(Integer.toString(id), category, name, pluginURL);
    }
    
    /**
     * Add a plugin configuration to a SynBioHub
     * 
     * @param category Type of plugin (rendering, submit, download)
     * @param name Name of the plugin
     * @param pluginURL URL for the plugin
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void addPluginConfig(String category, String name, String pluginURL) throws SynBioHubException
    {
    	savePluginConfig("New", category, name, pluginURL);
    }
    
    /**
     * Save a plugin configuration to a SynBioHub
     * 
     * @param id Id of plugin, if adding a plugin, id should be New
     * @param category Type of plugin (rendering, submit, download)
     * @param name Name of the plugin
     * @param pluginURL URL for the plugin
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    private void savePluginConfig(String id, String category, String name, String pluginURL) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to add a plugin configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/savePlugin";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("id", id));
        arguments.add(new BasicNameValuePair("category", category));
        arguments.add(new BasicNameValuePair("name", name));
        arguments.add(new BasicNameValuePair("url", pluginURL));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }   

    /**
     * Delete a plugin configuration to a SynBioHub
     * 
     * @param id Id of plugin
     * @param category Type of plugin (rendering, submit, download)
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void deletePluginConfig(int id, String category) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to delete a plugin configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/deletePlugin";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        id = id + 1;
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("id", Integer.toString(id)));
        arguments.add(new BasicNameValuePair("category", category));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }  
    
    /**
     * Get registries configuration for a SynBioHub
     *
     * @return A JSON object of the registries configuration for a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONObject getRegistriesConfig() throws SynBioHubException
    {
    	return getConfig("registries");
    }
    
    /**
     * Save a registry configuration for a SynBioHub
     * 
     * @param uriPrefix URI prefix for the registry
     * @param registryURL URL for the registry
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void saveRegistryConfig(String uriPrefix, String registryURL) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to save a registry configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/saveRegistry";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("uri", uriPrefix));
        arguments.add(new BasicNameValuePair("url", registryURL));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }   

    /**
     * Delete a registry configuration in a SynBioHub
     * 
     * @param uriPrefix URI prefix of the registry to delete
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void deleteRegistryConfig(String uriPrefix) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to remove a registry configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/deleteRegistry";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("uri", uriPrefix));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }
    
    /**
     * Update the administrator email configuration for a SynBioHub
     * 
     * @param administratorEmail Administrator email address
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void updateAdministratorEmailConfig(String administratorEmail) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to update the administrator email configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/setAdministratorEmail";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("administratorEmail", administratorEmail));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }   
    
    /**
     * Retrieve update from Web-of-Registries for a SynBioHub
     *   
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void retreiveUpdateFromWebOfRegistries() throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to retrieve update from Web-of-Registries.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/retrieveFromWebOfRegistries";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
	        
        try
        {
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    } 
    
    /**
     * Send request to join Web-of-Registries for a SynBioHub
     * 
     * @param administratorEmail Administrator email address
     * @param webOfRegistries URL for the Web-of-Registries
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void requestToJoinWebOfRegistries(String administratorEmail, String webOfRegistries) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to send request to join Web-of-Registries.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/federate";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Accept", "text/plain");
        
        List<NameValuePair> arguments = new ArrayList<>(4);
        arguments.add(new BasicNameValuePair("administratorEmail", administratorEmail));
        arguments.add(new BasicNameValuePair("webOfRegistries", webOfRegistries));
	        
        try
        {
            request.setEntity(new UrlEncodedFormEntity(arguments));
            HttpResponse response = client.execute(request);
            checkResponseCode(response);
        }
        catch (Exception e)
        {
        	//e.printStackTrace();
            throw new SynBioHubException(e);
            
        }
        finally
        {
            request.releaseConnection();
        }
    }   
    
    /**
     * Get remotes configuration for a SynBioHub
     *
     * @return A JSON object of the remotes configuration for a SynBioHub
     *
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */    
    public JSONObject getRemotesConfig() throws SynBioHubException
    {
    	return getConfig("remotes");
    }
    
    /**
     * Save a Benchling remote configuration for a SynBioHub
     * 
     * @param id Id of the Benchling remote
     * @param remoteURL URL for the Benchling remote
     * @param benchlingApiToken API token for the Benchling remote
     * @param rejectUnauthorized Check SSL certificate?
     * @param folderPrefix Prefix to use for folders on Benchling
     * @param sequenceSuffix Suffix to use for sequences found on Benchling
     * @param defaultFolderId Default folder on Benchling to access
     * @param isPublic Should the remote be visible publicly? 
     * @param rootCollectionDisplayId Display id for the root collection on the remote
     * @param rootCollectionName Name for the root collection on the remote
     * @param rootCollectionDescription Description for the root collection on the remote
     * 
     * @throws SynBioHubException if there was an error communicating with the SynBioHub
     */
    public void saveBenchlingRemoteConfig(String id, String remoteURL, String benchlingApiToken, 
    		boolean rejectUnauthorized, String folderPrefix, String sequenceSuffix, String defaultFolderId, 
    		boolean isPublic, String rootCollectionDisplayId, String rootCollectionName, 
    		String rootCollectionDescription) throws SynBioHubException
    {
    	if (user.equals("")) {
    		Exception e = new Exception("Must be logged in to save a Benchling remote configuration.");
    		throw new SynBioHubException(e);
    	}
        String url = backendUrl + "/admin/saveRemote";
    
        HttpPost request = new HttpPost(url);
        request.setHeader("X-authorization", user);
        request.setHeader("Ac…

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