webservices/compbio/ws/client/Services.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import java.io.File;\r
  22 import java.net.URL;\r
  23 import java.util.Set;\r
  24 \r
  25 import javax.xml.namespace.QName;\r
  26 import javax.xml.ws.Service;\r
  27 \r
  28 import compbio.data.msa.JABAService;\r
  29 import compbio.data.msa.MsaWS;\r
  30 import compbio.data.msa.SequenceAnnotation;\r
  31 import compbio.engine.client.ConfExecutable;\r
  32 import compbio.engine.client.Executable;\r
  33 import compbio.runner.conservation.AACon;\r
  34 import compbio.runner.disorder.Disembl;\r
  35 import compbio.runner.disorder.GlobPlot;\r
  36 import compbio.runner.disorder.IUPred;\r
  37 import compbio.runner.disorder.Jronn;\r
  38 import compbio.runner.msa.ClustalO;\r
  39 import compbio.runner.msa.ClustalW;\r
  40 import compbio.runner.msa.Mafft;\r
  41 import compbio.runner.msa.Muscle;\r
  42 import compbio.runner.msa.Probcons;\r
  43 import compbio.runner.msa.Tcoffee;\r
  44 \r
  45 /**\r
  46  * List of web services currently supported by JABAWS version 2\r
  47  * \r
  48  */\r
  49 public enum Services {\r
  50         MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS;\r
  51 \r
  52         public static Services getService(String servName) {\r
  53                 servName = servName.trim().toLowerCase();\r
  54                 for (Services service : Services.values()) {\r
  55                         if (service.toString().equalsIgnoreCase(servName)) {\r
  56                                 return service;\r
  57                         }\r
  58                 }\r
  59                 return null;\r
  60         }\r
  61 \r
  62         public static Services getServiceByRunner(\r
  63                         Class<Executable<?>> runnerClassName) {\r
  64                 assert runnerClassName != null;\r
  65                 String sname = runnerClassName.getSimpleName().toLowerCase();\r
  66                 for (Services service : Services.values()) {\r
  67                         if (service.toString().toLowerCase().contains(sname)) {\r
  68                                 return service;\r
  69                         }\r
  70                 }\r
  71                 return null;\r
  72         }\r
  73 \r
  74         public Class<? extends Executable<?>> getServiceImpl() {\r
  75                 switch (this) {\r
  76                         case AAConWS :\r
  77                                 return AACon.class;\r
  78                         case ClustalOWS :\r
  79                                 return ClustalO.class;\r
  80                         case ClustalWS :\r
  81                                 return ClustalW.class;\r
  82                         case MafftWS :\r
  83                                 return Mafft.class;\r
  84                         case MuscleWS :\r
  85                                 return Muscle.class;\r
  86                         case TcoffeeWS :\r
  87                                 return Tcoffee.class;\r
  88                         case ProbconsWS :\r
  89                                 return Probcons.class;\r
  90                         case DisemblWS :\r
  91                                 return Disembl.class;\r
  92                         case GlobPlotWS :\r
  93                                 return GlobPlot.class;\r
  94                         case JronnWS :\r
  95                                 return Jronn.class;\r
  96                         case IUPredWS :\r
  97                                 return IUPred.class;\r
  98                         default :\r
  99                                 throw new RuntimeException(\r
 100                                                 "Unknown web service implementation class for service: "\r
 101                                                                 + this);\r
 102                 }\r
 103         }\r
 104 \r
 105         public static Class<? extends Executable<?>> getRunnerByJobDirectory(\r
 106                         File jobdir) {\r
 107                 Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
 108                 return service.getServiceImpl();\r
 109         }\r
 110 \r
 111         private static String getRunnerNameByJobDirectory(File jobdir) {\r
 112                 String name = jobdir.getName().split("#")[0];\r
 113 \r
 114                 if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {\r
 115                         assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;\r
 116                         name = name.substring(1);\r
 117                 }\r
 118                 return name;\r
 119         }\r
 120 \r
 121         public static Services getServiceByJobDirectory(File jobdir) {\r
 122                 return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
 123         }\r
 124 \r
 125         private static Services getServiceByRunnerName(String name) {\r
 126                 for (Services service : Services.values()) {\r
 127                         String runnerName = service.getServiceImpl().getSimpleName()\r
 128                                         .toLowerCase();\r
 129                         name = name.trim().toLowerCase();\r
 130                         if (name.startsWith(runnerName)) {\r
 131                                 return service;\r
 132                         }\r
 133                 }\r
 134                 return null;\r
 135         }\r
 136 \r
 137         Service getService(URL url, String sqname) {\r
 138                 QName qname = new QName(sqname, this.toString());\r
 139                 return Service.create(url, qname);\r
 140         }\r
 141 \r
 142         public static String toString(Set<Services> services) {\r
 143                 if (services == null || services.isEmpty()) {\r
 144                         return "";\r
 145                 }\r
 146                 String value = "";\r
 147                 String delim = ", ";\r
 148                 for (Services serv : services) {\r
 149                         value += serv.toString() + delim;\r
 150                 }\r
 151                 value = value.substring(0, value.length() - delim.length());\r
 152                 return value;\r
 153         }\r
 154 \r
 155         Class<? extends JABAService> getServiceType() {\r
 156                 switch (this) {\r
 157                         // deliberate leaking\r
 158                         case AAConWS :\r
 159                         case JronnWS :\r
 160                         case DisemblWS :\r
 161                         case GlobPlotWS :\r
 162                         case IUPredWS :\r
 163                                 return SequenceAnnotation.class;\r
 164 \r
 165                                 // deliberate leaking\r
 166                         case ClustalWS :\r
 167                         case ClustalOWS :\r
 168                         case MafftWS :\r
 169                         case MuscleWS :\r
 170                         case ProbconsWS :\r
 171                         case TcoffeeWS :\r
 172 \r
 173                                 return MsaWS.class;\r
 174                         default :\r
 175                                 throw new RuntimeException("Unrecognised Web Service Type "\r
 176                                                 + this + " - Should never happened!");\r
 177                 }\r
 178         }\r
 179 \r
 180         JABAService getInterface(Service service) {\r
 181                 assert service != null;\r
 182 \r
 183                 QName portName = new QName(service.getServiceName().getNamespaceURI(),\r
 184                                 this.toString() + "Port");\r
 185                 return service.getPort(portName, this.getServiceType());\r
 186         }\r
 187 }