X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=webservices%2Fcompbio%2Fws%2Fserver%2FWSUtil.java;h=7341989581a7ddcb0907b40d4460680fbe172716;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=9895289706bb08d2c54260d1864f8d615829b7be;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 9895289..7341989 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -19,11 +19,14 @@ package compbio.ws.server;
 
 import java.security.InvalidParameterException;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.log4j.Logger;
 
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.ScoreManager;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.ProgressGetter;
@@ -34,14 +37,12 @@ import compbio.metadata.JobSubmissionException;
 import compbio.metadata.Limit;
 import compbio.metadata.LimitExceededException;
 import compbio.metadata.Option;
-import compbio.util.Timer;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.ws.client.Services;
+import compbio.ws.client.ServicesUtil;
 
 public final class WSUtil {
 
-	private static final String CACHE_KEY = "LIMITS_CACHE";
-
-	private static Logger log = Logger.getLogger(WSUtil.class);
-
 	public static final void validateJobId(String jobId)
 			throws InvalidParameterException {
 		if (!compbio.engine.client.Util.isValidJobId(jobId)) {
@@ -52,11 +53,25 @@ public final class WSUtil {
 	}
 
 	public static final void validateFastaInput(List<FastaSequence> sequences)
-			throws InvalidParameterException {
+			throws JobSubmissionException {
 		if (sequences == null || sequences.isEmpty()) {
-			throw new InvalidParameterException(
+			throw new JobSubmissionException(
 					"List of fasta sequences required but not provided! ");
 		}
+		Set<String> names = new HashSet<String>();
+		for (FastaSequence fs : sequences) {
+			boolean unique = names.add(fs.getId());
+			if (!unique) {
+				throw new JobSubmissionException(
+						"Input sequences must have unique names! \n"
+								+ "Sequence " + fs.getId() + " is a duplicate!");
+			}
+			if (fs.getLength() == 0) {
+				throw new JobSubmissionException(
+						"Sequence must not be empty! Sequence: " + fs.getId()
+								+ " was empty");
+			}
+		}
 	}
 
 	public static JobStatus getJobStatus(String jobId) {
@@ -83,19 +98,41 @@ public final class WSUtil {
 	}
 
 	public static <T> String align(List<FastaSequence> sequences,
-			ConfiguredExecutable<T> confExec, WSLogger logger,
+			ConfiguredExecutable<T> confExec, Logger logger,
 			String callingMethod, Limit<T> limit)
 			throws LimitExceededException, JobSubmissionException {
-		Timer timer = Timer.getMilliSecondsTimer();
+
 		if (limit != null && limit.isExceeded(sequences)) {
 			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
 		compbio.runner.Util.writeInput(sequences, confExec);
 		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
 		String jobId = engine.submitJob(confExec);
-		if (logger != null) {
-			logger.log(timer, callingMethod, jobId);
+		reportUsage(confExec, logger);
+		return jobId;
+	}
+
+	static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {
+		if (GAUtils.IS_GA_ENABLED) {
+			Services service = ServicesUtil.getServiceByRunner(confExec
+					.getExecutable().getClass());
+			GAUtils.reportUsage(service);
+			logger.info("Reporting GA usage for " + service);
+		}
+	}
+
+	public static <T> String analize(List<FastaSequence> sequences,
+			ConfiguredExecutable<T> confExec, Logger log, String method,
+			Limit<T> limit) throws JobSubmissionException {
+		if (limit != null && limit.isExceeded(sequences)) {
+			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
+		log.debug("Method: " + method + " with task: " + confExec.getTaskId());
+
+		compbio.runner.Util.writeInput(sequences, confExec);
+		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
+		String jobId = engine.submitJob(confExec);
+		reportUsage(confExec, log);
 		return jobId;
 	}
 
@@ -111,6 +148,36 @@ public final class WSUtil {
 		return oList;
 	}
 
+	public static void validateAAConInput(List<FastaSequence> sequences)
+			throws JobSubmissionException {
+		validateFastaInput(sequences);
+		int len = 0;
+		for (FastaSequence fs : sequences) {
+			if (len == 0) {
+				len = fs.getLength();
+				continue;
+			}
+			if (fs.getLength() != len) {
+				throw new JobSubmissionException(
+						"All sequences must be of the same length. Please align "
+								+ "the sequences prior to submission! The first sequence length is : "
+								+ len + " but the sequence '" + fs.getId()
+								+ "' length is " + fs.getLength());
+			}
+		}
+	}
+
+	public static <T> ScoreManager getAnnotation(String jobId, Logger log)
+			throws ResultNotAvailableException {
+		WSUtil.validateJobId(jobId);
+		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
+		ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine
+				.getResults(jobId);
+		ScoreManager mas = aacon.getResults();
+		log.trace(jobId + " getConservation : " + mas);
+		return mas;
+	}
+
 	/*
 	 * UNUSED
 	 *