-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
\r
import java.security.InvalidParameterException;\r
import java.util.ArrayList;\r
+import java.util.HashSet;\r
import java.util.List;\r
+import java.util.Set;\r
+\r
+import org.apache.log4j.Logger;\r
\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.ProgressGetter;\r
import compbio.metadata.Limit;\r
import compbio.metadata.LimitExceededException;\r
import compbio.metadata.Option;\r
-import compbio.util.Timer;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.ws.client.Services;\r
+import compbio.ws.client.ServicesUtil;\r
\r
public final class WSUtil {\r
\r
- public static final void validateJobId(String jobId)\r
- throws InvalidParameterException {\r
- if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
- throw new InvalidParameterException(\r
- "JobId is not provided or cannot be recognised! Given value: "\r
- + jobId);\r
+ public static final void validateJobId(String jobId)\r
+ throws InvalidParameterException {\r
+ if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
+ throw new InvalidParameterException(\r
+ "JobId is not provided or cannot be recognised! Given value: "\r
+ + jobId);\r
+ }\r
+ }\r
+\r
+ public static final void validateFastaInput(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ if (sequences == null || sequences.isEmpty()) {\r
+ throw new JobSubmissionException(\r
+ "List of fasta sequences required but not provided! ");\r
+ }\r
+ Set<String> names = new HashSet<String>();\r
+ for (FastaSequence fs : sequences) {\r
+ boolean unique = names.add(fs.getId());\r
+ if (!unique) {\r
+ throw new JobSubmissionException(\r
+ "Input sequences must have unique names! \n"\r
+ + "Sequence " + fs.getId() + " is a duplicate!");\r
+ }\r
+ if (fs.getLength() == 0) {\r
+ throw new JobSubmissionException(\r
+ "Sequence must not be empty! Sequence: " + fs.getId()\r
+ + " was empty");\r
+ }\r
+ }\r
}\r
- }\r
\r
- public static final void validateFastaInput(List<FastaSequence> sequences)\r
- throws InvalidParameterException {\r
- if (sequences == null || sequences.isEmpty()) {\r
- throw new InvalidParameterException(\r
- "List of fasta sequences required but not provided! ");\r
+ public static JobStatus getJobStatus(String jobId) {\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ return asyncEngine.getJobStatus(jobId);\r
}\r
- }\r
-\r
- public static JobStatus getJobStatus(String jobId) {\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- return asyncEngine.getJobStatus(jobId);\r
- }\r
-\r
- public static ChunkHolder pullFile(String file, long position) {\r
- return ProgressGetter.pull(file, position);\r
- }\r
-\r
- public static byte getProgress(String jobId) {\r
- throw new UnsupportedOperationException();\r
- }\r
-\r
- public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
- assert confClustal != null;\r
- return Configurator.getAsyncEngine(confClustal);\r
- }\r
-\r
- public static boolean cancelJob(String jobId) {\r
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- return asyncEngine.cancelJob(jobId);\r
- }\r
-\r
- public static <T> String align(List<FastaSequence> sequences,\r
- ConfiguredExecutable<T> confExec, WSLogger logger,\r
- String callingMethod, Limit<T> limit)\r
- throws LimitExceededException, JobSubmissionException {\r
- Timer timer = Timer.getMilliSecondsTimer();\r
- if (limit.isExceeded(sequences)) {\r
- throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+\r
+ public static ChunkHolder pullFile(String file, long position) {\r
+ return ProgressGetter.pull(file, position);\r
}\r
- compbio.runner.Util.writeInput(sequences, confExec);\r
- AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
- String jobId = engine.submitJob(confExec);\r
- if (logger != null) {\r
- logger.log(timer, callingMethod, jobId);\r
+\r
+ public static byte getProgress(String jobId) {\r
+ throw new UnsupportedOperationException();\r
+ }\r
+\r
+ public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
+ assert confClustal != null;\r
+ return Configurator.getAsyncEngine(confClustal);\r
}\r
- return jobId;\r
- }\r
-\r
- /*\r
- * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
- */\r
- public static final <T> List<String> getCommands(List<Option<T>> options,\r
- String keyValueSeparator) {\r
- List<String> oList = new ArrayList<String>();\r
- for (Option<T> o : options) {\r
- oList.add(o.toCommand(keyValueSeparator));\r
+\r
+ public static boolean cancelJob(String jobId) {\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ return asyncEngine.cancelJob(jobId);\r
+ }\r
+\r
+ public static <T> String align(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<T> confExec, Logger logger,\r
+ String callingMethod, Limit<T> limit)\r
+ throws LimitExceededException, JobSubmissionException {\r
+\r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\r
+ compbio.runner.Util.writeInput(sequences, confExec);\r
+ AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+ String jobId = engine.submitJob(confExec);\r
+ reportUsage(confExec, logger);\r
+ return jobId;\r
+ }\r
+ \r
+\r
+ static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
+ if (GAUtils.IS_GA_ENABLED) {\r
+ Services service = ServicesUtil.getServiceByRunner(confExec.getExecutable().getClass());\r
+ GAUtils.reportUsage(service);\r
+ logger.info("Reporting GA usage for " + service);\r
+ }\r
+ }\r
+\r
+ public static <T> String analize(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<T> confExec, Logger log, String method,\r
+ Limit<T> limit) throws JobSubmissionException {\r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\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 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
+ public static <T> String fold(List<FastaSequence> sequences,\r
+ ConfiguredExecutable<T> confExec, Logger log, String method,\r
+ Limit<T> limit) throws JobSubmissionException {\r
+ if (limit != null && limit.isExceeded(sequences)) {\r
+ throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+ }\r
+ compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
+ AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+ String jobId = engine.submitJob(confExec);\r
+ reportUsage(confExec, log);\r
+ return jobId;\r
+ }\r
+\r
+ /*\r
+ * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
+ */\r
+ public static final <T> List<String> getCommands(List<Option<T>> options,\r
+ String keyValueSeparator) {\r
+ List<String> oList = new ArrayList<String>();\r
+ for (Option<T> o : options) {\r
+ oList.add(o.toCommand(keyValueSeparator));\r
+ }\r
+ return oList;\r
+ }\r
+\r
+ public static void validateAAConInput(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ validateFastaInput(sequences);\r
+ int len = 0;\r
+ for (FastaSequence fs : sequences) {\r
+ if (len == 0) {\r
+ len = fs.getLength();\r
+ continue;\r
+ }\r
+ if (fs.getLength() != len) {\r
+ throw new JobSubmissionException(\r
+ "All sequences must be of the same length. Please align the sequences " + \r
+ " prior to submission! The first sequence length is : " + len + \r
+ " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
+ }\r
+ }\r
+ }\r
+\r
+ public static void validateJpredInput(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ validateFastaInput(sequences);\r
+ int len = 0;\r
+ for (FastaSequence fs : sequences) {\r
+ if (len == 0) {\r
+ len = fs.getLength();\r
+ continue;\r
+ }\r
+ if (fs.getLength() != len) {\r
+ System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());\r
+ throw new JobSubmissionException(\r
+ "All sequences must be of the same length. Please align the sequences " + \r
+ " prior to submission! The first sequence length is : " + len + \r
+ " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
+ }\r
+ }\r
+ }\r
+\r
+ public static <T> ScoreManager getAnnotation(String jobId, Logger log)\r
+ throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);\r
+ ScoreManager mas = aacon.getResults();\r
+ log.trace(jobId + " getConservation : " + mas);\r
+ return mas;\r
}\r
- return oList;\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff