\r
static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
if (GAUtils.IS_GA_ENABLED) {\r
- Services service = ServicesUtil.getServiceByRunner(confExec\r
- .getExecutable().getClass());\r
+ Services service = ServicesUtil.getServiceByRunner(confExec.getExecutable().getClass());\r
GAUtils.reportUsage(service);\r
logger.info("Reporting GA usage for " + service);\r
}\r
if (limit != null && limit.isExceeded(sequences)) {\r
throw LimitExceededException.newLimitExceeded(limit, sequences);\r
}\r
- log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
compbio.runner.Util.writeInput(sequences, confExec);\r
AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
String jobId = engine.submitJob(confExec);\r
reportUsage(confExec, log);\r
return jobId;\r
}\r
- \r
- // Same as analize but Alifold takes clustal input not fasta\r
+\r
+ // Same as analize(...) but RNAalifold takes clustal input not fasta\r
// An if condition in the above method might be a better solution but \r
// you need a way of finding out the type of confExec at runtime\r
\r
if (limit != null && limit.isExceeded(sequences)) {\r
throw LimitExceededException.newLimitExceeded(limit, sequences);\r
}\r
- log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
- // This line is different from the above method\r
compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
String jobId = engine.submitJob(confExec);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);\r
ScoreManager mas = aacon.getResults();\r
- \r
log.trace(jobId + " getConservation : " + mas);\r
return mas;\r
}\r
- \r
\r
- /*\r
- * UNUSED\r
- * \r
- * @SuppressWarnings("unchecked") static <T> LimitsManager<T>\r
- * getLimits(Class<? extends Executable<T>> clazz, WebServiceContext\r
- * wsContext) {\r
- * \r
- * String LIMIT_KEY = CACHE_KEY + clazz.getCanonicalName(); LimitsManager<T>\r
- * limit = (LimitsManager<T>) getObjectFromApplContext( LIMIT_KEY,\r
- * wsContext); if (limit == null) { synchronized (WSUtil.class) { limit =\r
- * (LimitsManager<T>) getObjectFromApplContext(LIMIT_KEY, wsContext); if\r
- * (limit == null) { limit = compbio.runner.Util\r
- * .getLimits((Class<Executable<T>>) clazz);\r
- * addObjectToApplContext(wsContext, LIMIT_KEY, limit); } } } return limit;\r
- * }\r
- * \r
- * static void addObjectToApplContext(WebServiceContext wsContext, String\r
- * objKey, Object obj) { assert !Util.isEmpty(objKey) :\r
- * "Key for the object must not be empty! "; assert wsContext != null;\r
- * \r
- * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
- * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); assert ctx !=\r
- * null; log.debug("Adding object with key '" + objKey + "' and value '" +\r
- * obj + "' to the application context"); ctx.setAttribute(objKey, obj); }\r
- * static Object getObjectFromApplContext(String objKey, WebServiceContext\r
- * wsContext) { assert !Util.isEmpty(objKey) :\r
- * "Key for the object must not be empty! "; assert wsContext != null;\r
- * \r
- * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
- * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); Object obj =\r
- * ctx.getAttribute(objKey); log.trace("Retrieving object with key '" +\r
- * objKey + "' and value '" + obj + "' from the application context");\r
- * return obj; }\r
- */\r
}\r