From 24b1f578d0752ca4e3ee410031af5678b3ff1189 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Mon, 14 Feb 2011 18:19:14 +0000
Subject: [PATCH] Change the way to deal with Limits to simplify wrapper
 writing and enable couping with null limits

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3751 e3abac25-378b-4346-85de-24260fe3988d
---
 datamodel/compbio/metadata/LimitsManager.java        |    3 +++
 engine/compbio/engine/client/SkeletalExecutable.java |    9 +++++++--
 runner/compbio/runner/Util.java                      |    3 +--
 webservices/compbio/ws/server/AAConWS.java           |    4 ++++
 webservices/compbio/ws/server/ClustalWS.java         |    5 +++++
 webservices/compbio/ws/server/DisemblWS.java         |    4 ++++
 webservices/compbio/ws/server/GlobPlotWS.java        |    4 ++++
 webservices/compbio/ws/server/JronnWS.java           |    3 +++
 webservices/compbio/ws/server/MafftWS.java           |    4 ++++
 webservices/compbio/ws/server/MuscleWS.java          |    4 ++++
 webservices/compbio/ws/server/ProbconsWS.java        |    4 ++++
 webservices/compbio/ws/server/TcoffeeWS.java         |    4 ++++
 12 files changed, 47 insertions(+), 4 deletions(-)

diff --git a/datamodel/compbio/metadata/LimitsManager.java b/datamodel/compbio/metadata/LimitsManager.java
index 92fd237..9e8dfb4 100644
--- a/datamodel/compbio/metadata/LimitsManager.java
+++ b/datamodel/compbio/metadata/LimitsManager.java
@@ -68,6 +68,9 @@ public class LimitsManager<T> {
 	 *         returned
 	 */
 	public Limit<T> getLimitByName(String presetName) {
+		if (limit == null) {
+			return null;
+		}
 		if (Util.isEmpty(presetName)) {
 			// return default limit
 			return getDefaultLimit();
diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index b289f6c..19fde7e 100644
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -293,11 +293,16 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	}
 
 	@Override
-	public Limit<T> getLimit(String presetName) {
-
+	public synchronized Limit<T> getLimit(String presetName) {
+		// Assume this function is called for the first time and thus need
+		// initialization
 		if (limits == null) {
 			limits = getLimits();
 		}
+		// Either the initialization failed or limits were not configured.
+		if (limits == null) {
+			return null;
+		}
 
 		Limit<T> limit = null;
 		if (limits != null) {
diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index 189ded7..bfced2a 100644
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -68,7 +68,7 @@ public final class Util {
 	 */
 
 	public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {
-		LimitsManager<T> limits = new LimitsManager<T>();
+		LimitsManager<T> limits = null;
 		try {
 			limits = ConfExecutable.getRunnerLimits(clazz);
 		} catch (FileNotFoundException e) {
@@ -80,7 +80,6 @@ public final class Util {
 			log.warn("IO exception while attempting to read limits for "
 					+ clazz + " executable! " + e.getLocalizedMessage(),
 					e.getCause());
-			return null;
 		}
 		return limits;
 	}
diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index ac7435d..8637af1 100644
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -84,6 +84,10 @@ public class AAConWS implements SequenceAnnotation<AACon> {
 
 	@Override
 	public Limit<AACon> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index f13136a..a5fc701 100644
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -155,10 +155,15 @@ public class ClustalWS implements MsaWS<ClustalW> {
 	@Override
 	public Limit<ClustalW> getLimit(String presetName) {
 		Timer timer = Timer.getMilliSecondsTimer();
+		if (limitMan == null) {
+			// No limit is configured
+			return null;
+		}
 		Limit<ClustalW> limit = limitMan.getLimitByName(presetName);
 		getLogger().logAll(timer, "getLimit");
 		return limit;
 	}
+
 	@Override
 	public LimitsManager<ClustalW> getLimits() {
 		return limitMan;
diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index 7970579..5c6bac5 100644
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -71,6 +71,10 @@ public class DisemblWS implements SequenceAnnotation<Disembl> {
 
 	@Override
 	public Limit<Disembl> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
index a77dfa2..b058882 100644
--- a/webservices/compbio/ws/server/GlobPlotWS.java
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -71,6 +71,10 @@ public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {
 
 	@Override
 	public Limit<GlobPlot> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index 5a4b136..b7a8f43 100644
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -73,6 +73,9 @@ public class JronnWS implements SequenceAnnotation<Jronn> {
 
 	@Override
 	public Limit<Jronn> getLimit(String presetName) {
+		if (limitMan == null) {
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index 0c8347d..83c5758 100644
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -127,6 +127,10 @@ public class MafftWS implements MsaWS<Mafft> {
 
 	@Override
 	public Limit<Mafft> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index c0de308..5b694dc 100644
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -126,6 +126,10 @@ public class MuscleWS implements MsaWS<Muscle> {
 
 	@Override
 	public Limit<Muscle> getLimit(String presetName) {
+		if (limitMan == null) {
+			// No limit is configured
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 85e8a70..bfad95a 100644
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -123,6 +123,10 @@ public class ProbconsWS implements MsaWS<Probcons> {
 
 	@Override
 	public Limit<Probcons> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index d8054b4..74c1723 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -137,6 +137,10 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 
 	@Override
 	public Limit<Tcoffee> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}
 
-- 
1.7.10.2