X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FWSUtil.java;h=89c73755a6ad8e663dcb67586109669b904da9a4;hb=b56011664ec5d11bb5d0cd09395e646586888700;hp=62996e521d709b0c67b26be0e1814ba382b97acc;hpb=fab6bab770b548a0c99ed6f5dfb46f5aa99f67c7;p=jabaws.git

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 62996e5..89c7375 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
@@ -19,37 +19,54 @@ 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.runner.RunnerUtil;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.ProgressGetter;
 import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.EngineUtil;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 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 {
 
 	public static final void validateJobId(String jobId)
 			throws InvalidParameterException {
-		if (!compbio.engine.client.Util.isValidJobId(jobId)) {
-			throw new InvalidParameterException(
-					"JobId is not provided or cannot be recognised! Given value: "
-							+ jobId);
+		if (!EngineUtil.isValidJobId(jobId)) {
+			throw new InvalidParameterException("JobId is not provided or cannot be recognised! Given value: " + jobId);
 		}
 	}
 
 	public static final void validateFastaInput(List<FastaSequence> sequences)
-			throws InvalidParameterException {
+			throws JobSubmissionException {
 		if (sequences == null || sequences.isEmpty()) {
-			throw new InvalidParameterException(
-					"List of fasta sequences required but not provided! ");
+			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! \nSequence " + fs.getId() + " is a duplicate!");
+			}
+			if (fs.getLength() == 0) {
+				throw new JobSubmissionException("Sequence must not be empty! Sequence: " + fs.getId() + " was empty");
+			}
 		}
 	}
 
@@ -77,19 +94,56 @@ 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);
+		RunnerUtil.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);
 		}
+		RunnerUtil.writeInput(sequences, confExec);
+		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
+		String jobId = engine.submitJob(confExec);
+		reportUsage(confExec, log);
+		return jobId;
+	}
+
+	// Same as analize(...) but RNAalifold takes clustal input not fasta
+	// An if condition in the above method might be a better solution but 
+	// you need a way of finding out the type of confExec at runtime
+	
+	public static <T> String fold(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);
+		}
+		RunnerUtil.writeClustalInput(sequences, confExec, '-');
+		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
+		String jobId = engine.submitJob(confExec);
+		reportUsage(confExec, log);
 		return jobId;
 	}
 
@@ -105,4 +159,51 @@ 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 void validateJpredInput(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) {
+				System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());
+				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;
+	}
+
 }