Change the way to deal with Limits to simplify wrapper writing and enable couping...
[jabaws.git] / webservices / compbio / ws / server / JronnWS.java
1 package compbio.ws.server;\r
2 \r
3 import java.io.File;\r
4 import java.util.List;\r
5 \r
6 import javax.annotation.Resource;\r
7 import javax.jws.WebService;\r
8 import javax.xml.ws.WebServiceContext;\r
9 \r
10 import org.apache.log4j.Logger;\r
11 \r
12 import compbio.data.msa.SequenceAnnotation;\r
13 import compbio.data.sequence.FastaSequence;\r
14 import compbio.data.sequence.ScoreManager;\r
15 import compbio.engine.AsyncExecutor;\r
16 import compbio.engine.Configurator;\r
17 import compbio.engine.client.ConfiguredExecutable;\r
18 import compbio.metadata.ChunkHolder;\r
19 import compbio.metadata.JobStatus;\r
20 import compbio.metadata.JobSubmissionException;\r
21 import compbio.metadata.Limit;\r
22 import compbio.metadata.LimitExceededException;\r
23 import compbio.metadata.LimitsManager;\r
24 import compbio.metadata.Option;\r
25 import compbio.metadata.Preset;\r
26 import compbio.metadata.PresetManager;\r
27 import compbio.metadata.ResultNotAvailableException;\r
28 import compbio.metadata.RunnerConfig;\r
29 import compbio.metadata.UnsupportedRuntimeException;\r
30 import compbio.metadata.WrongParameterException;\r
31 import compbio.runner.Util;\r
32 import compbio.runner.conservation.AACon;\r
33 import compbio.runner.disorder.Jronn;\r
34 \r
35 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
36 public class JronnWS implements SequenceAnnotation<Jronn> {\r
37 \r
38         // Ask for resource injection\r
39         @Resource\r
40         WebServiceContext wsContext;\r
41 \r
42         private static Logger statLog = Logger.getLogger("JronnWS-stats");\r
43 \r
44         private static Logger log = Logger.getLogger(JronnWS.class);\r
45 \r
46         private static final RunnerConfig<Jronn> jronnOptions = Util\r
47                         .getSupportedOptions(Jronn.class);\r
48 \r
49         private static final PresetManager<Jronn> jronnPresets = Util\r
50                         .getPresets(Jronn.class);\r
51 \r
52         private static final LimitsManager<Jronn> limitMan = compbio.runner.Util\r
53                         .getLimits(new Jronn().getType());\r
54 \r
55         ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
56                         throws JobSubmissionException {\r
57                 Jronn jronn = new Jronn();\r
58                 jronn.setInput("fasta.in").setOutput("jronn.out");\r
59                 return Configurator.configureExecutable(jronn, sequences);\r
60         }\r
61 \r
62         @Override\r
63         public ScoreManager getAnnotation(String jobId)\r
64                         throws ResultNotAvailableException {\r
65                 WSUtil.validateJobId(jobId);\r
66                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
67                 ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine\r
68                                 .getResults(jobId);\r
69                 ScoreManager mas = jronn.getResults();\r
70                 log.trace(jobId + " getConservation : " + mas);\r
71                 return mas;\r
72         }\r
73 \r
74         @Override\r
75         public Limit<Jronn> getLimit(String presetName) {\r
76                 if (limitMan == null) {\r
77                         return null;\r
78                 }\r
79                 return limitMan.getLimitByName(presetName);\r
80         }\r
81 \r
82         @Override\r
83         public LimitsManager<Jronn> getLimits() {\r
84                 return limitMan;\r
85         }\r
86 \r
87         @Override\r
88         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
89                 WSUtil.validateJobId(jobId);\r
90                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
91                                 + Jronn.getStatFile();\r
92                 return WSUtil.pullFile(file, position);\r
93         }\r
94 \r
95         @Override\r
96         public boolean cancelJob(String jobId) {\r
97                 WSUtil.validateJobId(jobId);\r
98                 return WSUtil.cancelJob(jobId);\r
99         }\r
100 \r
101         @Override\r
102         public JobStatus getJobStatus(String jobId) {\r
103                 WSUtil.validateJobId(jobId);\r
104                 return WSUtil.getJobStatus(jobId);\r
105         }\r
106 \r
107         @Override\r
108         public PresetManager<Jronn> getPresets() {\r
109                 return jronnPresets;\r
110         }\r
111 \r
112         @Override\r
113         public RunnerConfig<Jronn> getRunnerOptions() {\r
114                 return jronnOptions;\r
115         }\r
116 \r
117         String analize(List<FastaSequence> sequences,\r
118                         ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
119                         Limit<Jronn> limit) throws JobSubmissionException {\r
120                 if (limit != null && limit.isExceeded(sequences)) {\r
121                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
122                 }\r
123 \r
124                 compbio.runner.Util.writeInput(sequences, confExec);\r
125                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
126                 String jobId = engine.submitJob(confExec);\r
127                 return jobId;\r
128         }\r
129 \r
130         @Override\r
131         public String analize(List<FastaSequence> sequences)\r
132                         throws UnsupportedRuntimeException, LimitExceededException,\r
133                         JobSubmissionException {\r
134                 WSUtil.validateFastaInput(sequences);\r
135                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
136 \r
137                 return analize(sequences, confJronn, null, "analize", getLimit(""));\r
138         }\r
139 \r
140         @Override\r
141         public String customAnalize(List<FastaSequence> sequences,\r
142                         List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
143                         LimitExceededException, JobSubmissionException,\r
144                         WrongParameterException {\r
145                 WSUtil.validateFastaInput(sequences);\r
146                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
147 \r
148                 List<String> params = WSUtil.getCommands(options,\r
149                                 AACon.KEY_VALUE_SEPARATOR);\r
150                 confJronn.addParameters(params);\r
151                 return analize(sequences, confJronn, null, "customAnalize",\r
152                                 getLimit(""));\r
153         }\r
154 \r
155         @Override\r
156         public String presetAnalize(List<FastaSequence> sequences,\r
157                         Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
158                         LimitExceededException, JobSubmissionException,\r
159                         WrongParameterException {\r
160                 WSUtil.validateFastaInput(sequences);\r
161                 if (preset == null) {\r
162                         throw new WrongParameterException("Preset must be provided!");\r
163                 }\r
164                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
165                 confJronn.addParameters(preset.getOptions());\r
166                 Limit<Jronn> limit = getLimit(preset.getName());\r
167                 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
168         }\r
169 \r
170 }\r