1 package compbio.ws.server;
\r
4 import java.util.Arrays;
\r
5 import java.util.HashSet;
\r
6 import java.util.List;
\r
8 import javax.annotation.Resource;
\r
9 import javax.jws.WebService;
\r
10 import javax.xml.ws.WebServiceContext;
\r
12 import org.apache.log4j.Logger;
\r
14 import compbio.data.msa.Annotation;
\r
15 import compbio.data.sequence.FastaSequence;
\r
16 import compbio.data.sequence.Score;
\r
17 import compbio.engine.AsyncExecutor;
\r
18 import compbio.engine.Configurator;
\r
19 import compbio.engine.client.ConfiguredExecutable;
\r
20 import compbio.metadata.ChunkHolder;
\r
21 import compbio.metadata.JobStatus;
\r
22 import compbio.metadata.JobSubmissionException;
\r
23 import compbio.metadata.Limit;
\r
24 import compbio.metadata.LimitExceededException;
\r
25 import compbio.metadata.LimitsManager;
\r
26 import compbio.metadata.Option;
\r
27 import compbio.metadata.Preset;
\r
28 import compbio.metadata.PresetManager;
\r
29 import compbio.metadata.ResultNotAvailableException;
\r
30 import compbio.metadata.RunnerConfig;
\r
31 import compbio.metadata.UnsupportedRuntimeException;
\r
32 import compbio.metadata.WrongParameterException;
\r
33 import compbio.runner.Util;
\r
34 import compbio.runner.conservation.AACon;
\r
36 @WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")
\r
37 public class AAConWS implements Annotation<AACon> {
\r
39 // Ask for resource injection
\r
41 WebServiceContext wsContext;
\r
43 private static Logger statLog = Logger.getLogger("AAConWS-stats");
\r
45 private static Logger log = Logger.getLogger(AAConWS.class);
\r
47 private static final RunnerConfig<AACon> aaconOptions = Util
\r
48 .getSupportedOptions(AACon.class);
\r
50 private static final PresetManager<AACon> aaconPresets = Util
\r
51 .getPresets(AACon.class);
\r
53 ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
\r
54 throws JobSubmissionException {
\r
55 AACon aacon = new AACon();
\r
56 aacon.setInput("fasta.in").setOutput("aacon.out");
\r
57 return Configurator.configureExecutable(aacon, sequences);
\r
61 public HashSet<Score> getAnnotation(String jobId)
\r
62 throws ResultNotAvailableException {
\r
63 WSUtil.validateJobId(jobId);
\r
64 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
\r
65 ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
\r
67 HashSet<Score> mas = aacon.getResults();
\r
68 log.trace(jobId + " getConservation : " + mas);
\r
72 * @SuppressWarnings("unchecked") public JalviewAnnotation
\r
73 * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {
\r
74 * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //
\r
75 * log(jobId, "getResults"); return result.toJalviewAnnotation(); }
\r
79 public Limit<AACon> getLimit(String presetName) {
\r
80 return new AACon().getLimit(presetName);
\r
84 public LimitsManager<AACon> getLimits() {
\r
85 return new AACon().getLimits();
\r
89 public ChunkHolder pullExecStatistics(String jobId, long position) {
\r
90 WSUtil.validateJobId(jobId);
\r
91 String file = Configurator.getWorkDirectory(jobId) + File.separator
\r
92 + AACon.getStatFile();
\r
93 return WSUtil.pullFile(file, position);
\r
97 public boolean cancelJob(String jobId) {
\r
98 WSUtil.validateJobId(jobId);
\r
99 return WSUtil.cancelJob(jobId);
\r
103 public JobStatus getJobStatus(String jobId) {
\r
104 WSUtil.validateJobId(jobId);
\r
105 return WSUtil.getJobStatus(jobId);
\r
109 public PresetManager<AACon> getPresets() {
\r
110 return aaconPresets;
\r
114 public RunnerConfig<AACon> getRunnerOptions() {
\r
115 return aaconOptions;
\r
118 String analize(List<FastaSequence> sequences,
\r
119 ConfiguredExecutable<AACon> confExec, Logger log, String method,
\r
120 Limit<AACon> limit) throws JobSubmissionException {
\r
121 if (limit != null && limit.isExceeded(sequences)) {
\r
122 throw LimitExceededException.newLimitExceeded(limit, sequences);
\r
125 compbio.runner.Util.writeInput(sequences, confExec);
\r
126 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
\r
127 String jobId = engine.submitJob(confExec);
\r
132 public String analize(List<FastaSequence> sequences)
\r
133 throws UnsupportedRuntimeException, LimitExceededException,
\r
134 JobSubmissionException {
\r
135 WSUtil.validateFastaInput(sequences);
\r
136 ConfiguredExecutable<AACon> confAAcon = init(sequences);
\r
138 // set default conservation method to fastest - SHENKIN
\r
139 // TODO: This violates encapsulation, should be moved to the runners
\r
141 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));
\r
142 return analize(sequences, confAAcon, null, "analize", getLimit(""));
\r
146 public String customAnalize(List<FastaSequence> sequences,
\r
147 List<Option<AACon>> options) throws UnsupportedRuntimeException,
\r
148 LimitExceededException, JobSubmissionException,
\r
149 WrongParameterException {
\r
150 WSUtil.validateFastaInput(sequences);
\r
151 ConfiguredExecutable<AACon> confAACon = init(sequences);
\r
152 // Could not do that! Space separated values
\r
153 // will all be treated as keys! thus duplicates removed
\r
154 // String params = cbuilder.getCommand();
\r
155 List<String> params = WSUtil.getCommands(options,
\r
156 AACon.KEY_VALUE_SEPARATOR);
\r
157 confAACon.addParameters(params);
\r
158 return analize(sequences, confAACon, null, "customAnalize",
\r
163 public String presetAnalize(List<FastaSequence> sequences,
\r
164 Preset<AACon> preset) throws UnsupportedRuntimeException,
\r
165 LimitExceededException, JobSubmissionException,
\r
166 WrongParameterException {
\r
167 WSUtil.validateFastaInput(sequences);
\r
168 if (preset == null) {
\r
169 throw new WrongParameterException("Preset must be provided!");
\r
171 ConfiguredExecutable<AACon> confAAcon = init(sequences);
\r
172 confAAcon.addParameters(preset.getOptions());
\r
173 Limit<AACon> limit = getLimit(preset.getName());
\r
174 return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);
\r