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prem0862/boost-tasks

Created August 7, 2018 05:11
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boost-tasks
package edu.utah.ece.async.sboldesigner.boost;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URI;
import java.util.Set;
import org.json.JSONException;
import org.json.JSONObject;
import org.sbolstandard.core2.ComponentDefinition;
import org.sbolstandard.core2.SBOLConversionException;
import org.sbolstandard.core2.SBOLDocument;
import org.sbolstandard.core2.SBOLValidationException;
import com.google.common.eventbus.EventBus;
import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLDesign;
import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
import gov.doe.jgi.boost.client.BOOSTClient;
import gov.doe.jgi.boost.client.utils.DocumentConversionUtils;
import gov.doe.jgi.boost.client.utils.JsonResponseParser;
import gov.doe.jgi.boost.enums.FileFormat;
import gov.doe.jgi.boost.enums.Strategy;
import gov.doe.jgi.boost.enums.Vendor;
import gov.doe.jgi.boost.exception.BOOSTBackEndException;
import gov.doe.jgi.boost.exception.BOOSTClientException;
public class BOOSTOperations {
private static EventBus eventBus = null;
static BOOSTClient client = new BOOSTClient(new BOOSTPreferences().getBOOSTToken());
static String targetNamespace = SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString();
public static void codonJuggling(SBOLDocument currentDesign, boolean annotation, Strategy strategy, String host) {
String codonJuggleJobUUID = null;
JSONObject jobReport = null;
eventBus = new EventBus();
try {
codonJuggleJobUUID = client.codonJuggle(
currentDesign, // input sequences
targetNamespace,
annotation, // exclusively 5'-3' coding sequences
strategy, // codon selection strategy
host, // predefined host
FileFormat.SBOL);
} catch (JSONException | SBOLConversionException | BOOSTClientException |
BOOSTBackEndException | IOException e) {
e.printStackTrace();
}
if (codonJuggleJobUUID != null) {
jobReport = checkJobReport(codonJuggleJobUUID);
String response = JsonResponseParser.parseCodonJuggleResponse(jobReport);
try {
Set<URI> rootUri = null;
Set<URI> comDefRoles = null;
SBOLDocument modifiedDocument = DocumentConversionUtils.stringToSBOLDocument(response);
// fetch root ComponentDefination of modifiedDocument
Set<ComponentDefinition> componentDef = modifiedDocument.getRootComponentDefinitions();
for (ComponentDefinition componentDefination : componentDef) {
comDefRoles = componentDefination.getRoles();
rootUri = componentDefination.getWasDerivedFroms();
System.out.println(rootUri);
}
System.out.println(comDefRoles);
for(URI designURI : rootUri) {
if(null != designURI) {
System.out.println("Prepared to call load method");
System.out.println(designURI);
new SBOLDesign(eventBus).load(modifiedDocument, designURI);
}
}
} catch (SBOLValidationException | IOException | SBOLConversionException e) {
e.printStackTrace();
}
}
}
public static void dnaVerification(SBOLDocument currentDesign, Vendor vendor, String sequencePatternsFilename) {
String dnaVarificationJobUUID = null;
JSONObject jobReport = null;
try {
dnaVarificationJobUUID = client.dnaVerification(
currentDesign,
targetNamespace,
vendor,
sequencePatternsFilename);
} catch (JSONException | SBOLConversionException | BOOSTClientException |
BOOSTBackEndException | IOException e) {
e.printStackTrace();
}
if (dnaVarificationJobUUID != null) {
jobReport = checkJobReport(dnaVarificationJobUUID);
String response = jobReport.toString();
System.out.println(response);
}
}
public static void polishing(SBOLDocument currentDesign, boolean annotation, Vendor vendor, Strategy strategy, String host) {
String polishDNAJobUUID = null;
JSONObject jobReport = null;
try {
polishDNAJobUUID = client.polish(
currentDesign, // input sequence
targetNamespace,
annotation, // encoding sequences support sequence feature annotations
vendor, // vendor
strategy, // codon selection strategy
FileFormat.SBOL, // output format
host);
} catch (JSONException | UnsupportedEncodingException | SBOLConversionException |
BOOSTClientException | BOOSTBackEndException e) {
e.printStackTrace();
}
if (polishDNAJobUUID != null) {
jobReport = checkJobReport(polishDNAJobUUID);
}
}
public static void partition(SBOLDocument currentDesign, String fivePrimeVectorOverlap, String threePrimeVectorOverlap,
String minLengthBB, String maxLengthBB, String minSeqOverlap, String optSeqOverlap,
String maxSeqOverlap, String minOverlapGC, String optOverlapGC, String maxOverlapGC,
String minPrimerLength, String optPrimerLength, String maxPrimerLength) {
String partitionDNAJobUUID = null;
JSONObject jobReport = null;
try {
partitionDNAJobUUID = client.partition(
currentDesign,
targetNamespace,
fivePrimeVectorOverlap,
threePrimeVectorOverlap,
minLengthBB,
maxLengthBB,
minOverlapGC,
optOverlapGC,
maxOverlapGC,
minSeqOverlap,
optSeqOverlap,
maxSeqOverlap,
minPrimerLength,
optPrimerLength,
maxPrimerLength);
} catch (JSONException | UnsupportedEncodingException | BOOSTClientException | BOOSTBackEndException
| SBOLConversionException e) {
e.printStackTrace();
}
if (partitionDNAJobUUID != null) {
jobReport = checkJobReport(partitionDNAJobUUID);
}
}
static JSONObject checkJobReport(String jobUUID) {
JSONObject jobReport = null;
try {
while (null == (jobReport = client.getJobReport(jobUUID))) {
// if the job isn't finished, then we wet some seconds
// and check again
System.out.println("Job " + jobUUID + " is not finished yet.");
try {
Thread.sleep(5000);
} catch (Exception e) {
}
}
} catch (BOOSTClientException | BOOSTBackEndException e) {
e.printStackTrace();
}
return jobReport;
}
}
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