import java.io.File;\r
import java.io.FileInputStream;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
import java.util.Arrays;\r
import java.util.logging.Level;\r
import java.util.logging.Logger;\r
\r
+import javax.xml.namespace.QName;\r
import javax.xml.ws.Service;\r
import javax.xml.ws.WebServiceException;\r
\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
+import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
public class Jws2Client {\r
\r
/*\r
- * Use java.util.Logger instead of log4j logger to reduce the size of the\r
- * client package\r
+ * TODO Use java.util.Logger instead of log4j logger to reduce the size of\r
+ * the client package\r
*/\r
private static final Logger log = Logger.getLogger(Jws2Client.class\r
.getCanonicalName());\r
}\r
Alignment alignment = null;\r
if (inputFile != null) {\r
- if (service == Services.AAConWS) {\r
- System.out.println("calc conserv!");\r
+ Writer writer = null;\r
+ if (outFile != null) {\r
+ writer = IOHelper.getWriter(outFile);\r
} else {\r
+ // this stream is going to be closed later which is fine as\r
+ // std.out will not be\r
+ writer = new PrintWriter(System.out, true);\r
+ }\r
+ if (service.getServiceType() == SequenceAnnotation.class) {\r
+ ScoreManager result = analize(inputFile,\r
+ ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
\r
+ IOHelper.writeOut(writer, result);\r
+ } else {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
- OutputStream outStream = null;\r
- if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
- } else {\r
- // this stream is going to be closed later which is fine as\r
- // std.out will not be\r
- outStream = System.out;\r
- }\r
- IOHelper.writeOut(outStream, alignment);\r
- // stream is closed in the method no need to close it here\r
+ IOHelper.writeOut(writer, alignment);\r
}\r
+ writer.close();\r
}\r
\r
boolean listParameters = CmdHelper.listParameters(cmd);\r
((Closeable) msaws).close();\r
log.fine("Disconnected successfully!");\r
}\r
+ /**\r
+ * Calculate conservation for sequences loaded from the file\r
+ * \r
+ * @param wsproxy\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws UnknownFileFormatException\r
+ */\r
+ static <T> ScoreManager analize(List<FastaSequence> fastalist,\r
+ SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+\r
+ ScoreManager scores = null;\r
+ try {\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out\r
+ .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = wsproxy.customAnalize(fastalist, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = wsproxy.presetAnalize(fastalist, preset);\r
+ } else {\r
+ jobId = wsproxy.analize(fastalist);\r
+ }\r
+ System.out.println("\n\ncalling analise.........");\r
+ Thread.sleep(1000);\r
+ scores = wsproxy.getAnnotation(jobId);\r
+\r
+ } catch (JobSubmissionException e) {\r
+ System.err\r
+ .println("Exception while submitting job to a web server. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException e) {\r
+ // ignore and propagate an interruption\r
+ Thread.currentThread().interrupt();\r
+ System.err.println("Exception while waiting for results. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (WrongParameterException e) {\r
+ System.err\r
+ .println("Exception while parsing the web method input parameters. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ }\r
+ return scores;\r
+\r
+ }\r
\r
/**\r
+ * Calculate conservation for sequences loaded from the file\r
+ * \r
+ * @param wsproxy\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws IOException\r
+ * @throws UnknownFileFormatException\r
+ */\r
+ static <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
+ Preset<T> preset, List<Option<T>> customOptions) {\r
+ List<FastaSequence> fastalist = null;\r
+ try {\r
+ fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+ assert !fastalist.isEmpty() : "Input is empty!";\r
+ } catch (IOException e) {\r
+ System.err\r
+ .println("Exception while reading the input file. "\r
+ + "Check that the input file contains a list of fasta formatted sequences! "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err\r
+ .println("Exception while attempting to read the input file "\r
+ + "Exception details are below:");\r
+ System.out.println(e.getMessage());\r
+ e.printStackTrace();\r
+ }\r
+ return analize(fastalist, wsproxy, preset, customOptions);\r
+ }\r
+ /**\r
* Connects to a web service by the host and the service name\r
* \r
* @param T\r
try {\r
serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
} catch (WebServiceException wse) {\r
- System.out.println("Conecting to JABAWS version 2 service");\r
+ System.out.println("Connecting to JABAWS version 2 service");\r
if (isV2service(wse)) {\r
serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
}\r
}\r
+ if (serv == null) {\r
+ System.err.println("Could not connect to " + url\r
+ + " the server is down?");\r
+ // FIXME\r
+ }\r
JABAService serviceIF = service.getInterface(serv);\r
- log.log(Level.FINE, "Connected successfully!");\r
+ log.log(Level.INFO, "Connected successfully!");\r
\r
return serviceIF;\r
}\r
return false;\r
}\r
\r
+ public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
+ throws WebServiceException {\r
+ URL url = null;\r
+ String service = "RegistryWS";\r
+ log.log(Level.FINE, "Attempting to connect...");\r
+\r
+ try {\r
+ url = new URL(host + "/" + service + "?wsdl");\r
+ } catch (MalformedURLException e) {\r
+ e.printStackTrace();\r
+ // ignore as the host name is already verified\r
+ }\r
+ QName qname = new QName(V2_QUALIFIED_SERVICE_NAME, service);\r
+ Service serv = Service.create(url, qname);\r
+\r
+ if (serv == null) {\r
+ System.err.println("Could not connect to " + url\r
+ + " the server is down?");\r
+ }\r
+\r
+ QName portName = new QName(serv.getServiceName().getNamespaceURI(),\r
+ service + "Port");\r
+ compbio.data.msa.RegistryWS serviceIF = serv.getPort(portName,\r
+ compbio.data.msa.RegistryWS.class);\r
+\r
+ log.log(Level.INFO, "Connected to " + service + " successfully!");\r
+\r
+ return serviceIF;\r
+ }\r
+\r
/**\r
* Align sequences from the file using MsaWS\r
* \r
} else {\r
jobId = msaws.align(fastalist);\r
}\r
+ System.out.println("\n\ncalling align.........");\r
Thread.sleep(1000);\r
alignment = msaws.getResult(jobId);\r
\r
\r
/**\r
* Starts command line client, if no parameter are supported print help. Two\r
- * parameters are required for successfull call the JWS2 host name and a\r
+ * parameters are required for successful call the JWS2 host name and a\r
* service name.\r
* \r
* @param args\r
git://source.jalview.org / jabaws.git / blobdiff