-package compbio.ws.server;
-
-import java.io.File;
-import java.util.List;
-
-import javax.jws.WebParam;
-import javax.jws.WebService;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.msa.FoldWS;
-import compbio.data.msa.JABAService;
-import compbio.data.msa.JManagement;
-import compbio.data.msa.Metadata;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAstruct;
-import compbio.data.sequence.FastaSequence;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
-import compbio.runner.structure.RNAalifold;
-
-@WebService(endpointInterface = "compbio.data.msa.FoldWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
-public class RNAalifoldWS implements FoldWS<RNAalifold> {
-
- private static Logger log = Logger.getLogger(ClustalWS.class);
-
- private static final RunnerConfig<RNAalifold> rnaalifoldOptions = Util.
- getSupportedOptions(RNAalifold.class);
-
- private static final PresetManager<RNAalifold> rnaalifoldPresets = Util
- .getPresets(RNAalifold.class);
-
- private static final LimitsManager<RNAalifold> limitMan = compbio.engine.client.Util
- .getLimits(new RNAalifold().getType());
-
-
- @Override
- public String fold(Alignment alignment)
- throws JobSubmissionException {
-
- // Validate clustal input here?
- ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
- return WSUtil.fold(alignment, confRNAalifold, log, "fold", getLimit(""));
- }
-
-
- ConfiguredExecutable<RNAalifold> init(Alignment dataset) throws JobSubmissionException {
- RNAalifold rnaalifold = new RNAalifold();
- rnaalifold.setInput(SkeletalExecutable.INPUT)
- .setOutput(SkeletalExecutable.OUTPUT)
- .setError(SkeletalExecutable.ERROR);
- ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
- .configureExecutable(rnaalifold, dataset.getSequences());
- return confRNAalifold;
- }
-
- @Override
- public String presetFold(Alignment alignment,
- Preset<RNAalifold> preset) throws JobSubmissionException,
- WrongParameterException {
- // validate
- if (preset == null) {
- throw new WrongParameterException("Preset must be Provided!");
- }
- Limit<RNAalifold> limit = getLimit(preset.getName());
- ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
- confRNAalifold.addParameters(preset.getOptions());
- return WSUtil.fold(alignment, confRNAalifold, log, "presetFold", limit);
- }
-
- @Override
- public String customFold(Alignment alignment,
- List<Option<RNAalifold>> options) throws JobSubmissionException,
- WrongParameterException {
- // validate
- ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
- List<String> params = WSUtil.getCommands(options,
- RNAalifold.KEY_VALUE_SEPARATOR);
- confRNAalifold.addParameters(params);
- log.info("Setting parameters: " + params);
- return WSUtil.fold(alignment, confRNAalifold, log, "customFold",
- getLimit(""));
- }
-
- @Override
- public RunnerConfig<RNAalifold> getRunnerOptions() {
- return rnaalifoldOptions;
- }
-
- @SuppressWarnings("unchecked")
- public RNAstruct getResult(String jobId) throws ResultNotAvailableException {
-
- WSUtil.validateJobId(jobId);
- AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
- ConfiguredExecutable<RNAalifold> rnaalifold = (ConfiguredExecutable<RNAalifold>) asyncEngine
- .getResults(jobId);
- return rnaalifold.getResults();
- }
-
- @Override
- public boolean cancelJob(String jobId) {
- WSUtil.validateJobId(jobId);
- boolean result = WSUtil.cancelJob(jobId);
- return result;
- }
-
- @Override
- public JobStatus getJobStatus(String jobId) {
- WSUtil.validateJobId(jobId);
- JobStatus status = WSUtil.getJobStatus(jobId);
- return status;
- }
-
- @Override
- public Limit<RNAalifold> getLimit(String presetName) {
- if (limitMan == null) {
- // No limit is configured
- return null;
- }
- Limit<RNAalifold> limit = limitMan.getLimitByName(presetName);
- return limit;
- }
-
- @Override
- public LimitsManager<RNAalifold> getLimits() {
- return limitMan;
- }
-
- @Override
- // PlaceHolder
- public PresetManager<RNAalifold> getPresets() {
- if (rnaalifoldPresets == null) {
- // No presets are configured
- return null;
- }
- return rnaalifoldPresets;
- }
-
- @Override
- // PlaceHolder
- public ChunkHolder pullExecStatistics(String jobId, long position) {
-
-// WSUtil.validateJobId(jobId);
-// String file = Configurator.getWorkDirectory(jobId) + File.separator
-// + RNAalifold.getStatFile();
-// ChunkHolder cholder = WSUtil.pullFile(file, position);
-// return cholder;
- return new ChunkHolder("", -1);
- }
-}
-
-
+package compbio.ws.server;\r
+\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")\r
+public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> \r
+ implements\r
+ SequenceAnnotation<RNAalifold> {\r
+\r
+ private static Logger log = Logger.getLogger(RNAalifoldWS.class);\r
+ \r
+ public RNAalifoldWS() {\r
+ super (new RNAalifold(), log);\r
+ }\r
+ \r
+ // Only purpose is to replace "analize" with "fold" method \r
+ // so that a clustal input file and not fasta will be generated\r
+ @Override\r
+ public String analize(List<FastaSequence> sequences)\r
+ throws UnsupportedRuntimeException, LimitExceededException,\r
+ JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "analize",\r
+ getLimit(""));\r
+ }\r
+\r
+ // Only purpose is to replace "analize" with "fold" method \r
+ // so that a clustal input file and not fasta will be generated\r
+ @Override\r
+ public String customAnalize(List<FastaSequence> sequences,\r
+ List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
+ \r
+ List<String> params = WSUtil.getCommands(options,\r
+ AACon.KEY_VALUE_SEPARATOR);\r
+ confRNAalifold.addParameters(params);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
+ getLimit(""));\r
+ }\r
+ \r
+ \r
+ /*\r
+ * No presets are supported, thus the result of this call will be as simple\r
+ * call to analize without parameters\r
+ */\r
+ @Override\r
+ public String presetAnalize(List<FastaSequence> sequences,\r
+ Preset<RNAalifold> preset) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+\r
+ return analize(sequences);\r
+ }\r
+}\r
+ \r
+ \r
git://source.jalview.org / jabaws.git / blobdiff