X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fws%2Fjpred%2FJpredWS.java;h=5249280f4fb53465b6bd5abd010e4f735a03de24;hb=d533fe6c1adf9f81009386ce42a9beb6999f7c3c;hp=16e100fee07cb6a14339b9aebc0d8e4c719fd454;hpb=db6ea93133979ad97453a89fac0506b69d104ea6;p=proteocache.git

diff --git a/server/compbio/ws/jpred/JpredWS.java b/server/compbio/ws/jpred/JpredWS.java
index 16e100f..5249280 100644
--- a/server/compbio/ws/jpred/JpredWS.java
+++ b/server/compbio/ws/jpred/JpredWS.java
@@ -1,27 +1,95 @@
 package compbio.ws.jpred;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
 import javax.jws.WebService;
 
 import org.apache.log4j.Logger;
 
+import compbio.beans.ProteinBean;
 import compbio.cassandra.CassandraNativeConnector;
 import compbio.cassandra.readers.SequenceReader;
+import compbio.engine.archive.ArchivedJob;
 
+/**
+ * Implementation of the Jpred web service in ProteoCache
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @version 1.0
+ * @since Jan 2014
+ */
 @WebService(endpointInterface = "compbio.ws.jpred.Jpred", targetNamespace = "http://server.proteocache.ws", serviceName = "ProteoCacheWS", portName = "ProteoCacheWSPort")
 public class JpredWS implements Jpred {
 	private static Logger log = Logger.getLogger(CassandraNativeConnector.class);
+	String jobid;
 
-	@Override
-	public String findSequence(String sequence, String program, String version) {
+	private List<String> findJobs(String sequence, String program, String version) {
 		CassandraNativeConnector dbconnector = new CassandraNativeConnector();
 		SequenceReader reader = new SequenceReader();
 		reader.setSession(dbconnector.getSession());
-		log.debug("ProteoCacheWS is connected:\n search for sequence: " + sequence + "\ncalculated wih  " + program + " (version; "
+		log.debug("ProteoCacheWS is connected:\n search for sequence: " + sequence + "\ncalculated with  " + program + " (version: "
 				+ version + ")");
-		if (null != reader.readProteins(sequence, "whole")) {
-			return "The sequence " + sequence + " found. Calculated with " + program + "(" + version + ")";
+		List<String> jobs = new ArrayList<String>();
+		List<ProteinBean> result = reader.readProteins(sequence, "whole");
+		if (null != result) {
+			for (ProteinBean protein : result) {
+				List<String> thejobs = protein.getJobid();
+				jobid = thejobs.get(0);
+				for (String job : thejobs) {
+					jobs.add(job);
+				}
+			}
+		}
+		return jobs;
+	}
+
+	@Override
+	public String findSequence(String sequence, String program, String version) {
+		List<String> jobs = findJobs(sequence, program, version);
+		if (null != jobs) {
+			return jobs.size() + " jobs found";
+		}
+		return "no jobs found";
+	}
+
+	@Override
+	public String findJobForSequence(String sequence, String program, String version) {
+		List<String> jobs = findJobs(sequence, program, version);
+		if (null != jobs) {
+			for (String job : jobs) {
+				String link = null;
+				ArchivedJob aj = new ArchivedJob(job);
+				try {
+					link = aj.prepareJobArchiveToWeb();
+				} catch (IOException e) {
+					log.error("JpredWS.findSequence: IO exception with job archive file");
+					log.error(e.getLocalizedMessage(), e.getCause());
+				}
+				if (null != link) {
+					return job;
+				}
+			}
+			return "";
+		}
+		return "";
+	}
+
+	@Override
+	public String getArchive(String jobid) {
+		String link = null;
+		ArchivedJob aj = new ArchivedJob(jobid);
+		try {
+			link = aj.prepareJobArchiveToWeb();
+		} catch (IOException e) {
+			log.error("JpredWS.findSequence: IO exception with job archive file");
+			log.error(e.getLocalizedMessage(), e.getCause());
 		}
-		return "The sequence " + sequence + " not found";
+		// if the archive file is not available null is returned
+		return link;
 	}
 
 }