Remove still unsupported methods of RegistryWS

[jabaws.git] / webservices / compbio / ws / client / Jws2Client.java

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index eac049e..cf0cf23 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -27,7 +27,6 @@ import java.io.File;
 import java.io.FileInputStream;\r
 import java.io.FileOutputStream;\r
 import java.io.IOException;\r
-import java.io.OutputStream;\r
 import java.io.PrintWriter;\r
 import java.io.Writer;\r
 import java.net.ConnectException;\r
@@ -57,8 +56,11 @@ import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.JobStatus;\r
 import compbio.metadata.Option;\r
+import compbio.metadata.Limit;\r
 import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.WrongParameterException;\r
 import compbio.util.FileUtil;\r
@@ -176,7 +178,7 @@ public class Jws2Client {
                                Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);\r
                                if (serviceName.equalsIgnoreCase("JpredWS")) {\r
                                        writer.close();\r
-                                       JpredAlignment jpred = new JpredAlignment(alignment.getSequences(), alignment.getMetadata());\r
+                                       JpredAlignment jpred = (JpredAlignment)alignment;\r
                                        if (outfile != null) {\r
                                                FileOutputStream fout = new FileOutputStream(outfile);\r
                                                SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r
@@ -188,17 +190,30 @@ public class Jws2Client {
                                        IOHelper.writeOut(writer, alignment);\r
                                        writer.close();\r
                                }\r
+                               AlignmentMetadata md = alignment.getMetadata();\r
+                               System.out.println("Output has been prepared with " + md.getProgram());\r
                        }\r
                }\r
 \r
                if (CmdHelper.listParameters(cmd)) {\r
-                       System.out.println(MetadataHelper.getParametersList(thews));\r
+                       List<Option<T>> opts = MetadataHelper.getParametersList(thews, hostname);\r
+                       for (Option<T> o : opts) {\r
+                               System.out.println("##############################################################################\n" + o.toString());\r
+                       }\r
                }\r
                if (CmdHelper.listPresets(cmd)) {\r
-                       System.out.println(MetadataHelper.getPresetList(thews));\r
+                       PresetManager<T> psm = MetadataHelper.getPresetList(thews);\r
+                       if (null != psm) {\r
+                               System.out.print(psm);\r
+                       } else {\r
+                               System.out.println("No presets are defined for the Web service");\r
+                       }\r
                }\r
                if (CmdHelper.listLimits(cmd)) {\r
-                       System.out.println(MetadataHelper.getLimits(thews));\r
+                       List<Limit<T>> lims = MetadataHelper.getLimits(thews);\r
+                       for (Limit<T> l : lims) {\r
+                               System.out.println("##############################################################################\n" + l.toString());\r
+                       }\r
                }\r
                log.fine("Disconnecting...");\r
                ((Closeable) thews).close();\r
@@ -306,11 +321,11 @@ public class Jws2Client {
 \r
        private static void listAllServices(String hostname) throws WebServiceException, IOException {\r
                RegistryWS registry = connectToRegistry(hostname);\r
-               Set<Services> func_services = Collections.EMPTY_SET;\r
-               Set<Services> nonfunc_services = Collections.EMPTY_SET;\r
+               Set<Services> func_services = Collections.emptySet();\r
+               //Set<Services> nonfunc_services = Collections.emptySet();\r
                if (registry != null) {\r
                        func_services = registry.getSupportedServices();\r
-                       nonfunc_services = registry.getNonoperatedServices();\r
+                       //nonfunc_services = registry.getNonoperatedServices();\r
                        FileUtil.closeSilently(((Closeable) registry));\r
                } else {\r
                        System.out.println("Failed to connect to the registry! ");\r
@@ -321,11 +336,13 @@ public class Jws2Client {
                        String mess = "\n\rThe list:\n";\r
                        System.out.println(mess + Services.toString(func_services));\r
                }\r
+               /*\r
                if (!nonfunc_services.isEmpty()) {\r
                        System.out.println("There are " + nonfunc_services.size() + " non-available services at " + hostname + ":");\r
                        String mess = "The list (internal tests failed): ";\r
                        System.out.println(mess + Services.toString(nonfunc_services));\r
                }\r
+               */\r
        }\r
 \r
        /**\r
@@ -358,6 +375,8 @@ public class Jws2Client {
                        }\r
                        System.out.println("\n\rcalling predictor.........");\r
                        Thread.sleep(100);\r
+                       JobStatus status = wsproxy.getJobStatus(jobId);\r
+                       System.out.println("\njob " + jobId + " status: " + status);\r
                        scores = wsproxy.getAnnotation(jobId);\r
                } catch (JobSubmissionException e) {\r
                        System.err.println("Exception while submitting job to a web server. Exception details are below:");\r
@@ -446,7 +465,12 @@ public class Jws2Client {
                                jobId = msaws.align(fastalist);\r
                        }\r
                        System.out.println("\ncalling program.........");\r
-                       Thread.sleep(100);\r
+                       long startTime = System.nanoTime();\r
+                       while (JobStatus.RUNNING == msaws.getJobStatus(jobId)) {\r
+                               Thread.sleep(1000);\r
+                               long endTime = System.nanoTime();\r
+                               System.out.println("job " + jobId + " time executing: "+ (endTime - startTime) / 1000000 +" msec, status: " + msaws.getJobStatus(jobId));\r
+                       }\r
                        alignment = msaws.getResult(jobId);\r
                } catch (IOException e) {\r
                        System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "\r
@@ -512,7 +536,6 @@ public class Jws2Client {
         * \r
         */\r
        public static void main(String[] args) {\r
-\r
                if (args == null) {\r
                        System.out.println(Constraints.help_text);\r
                        System.exit(1);\r
@@ -522,7 +545,6 @@ public class Jws2Client {
                        System.out.println(Constraints.help_text);\r
                        System.exit(1);\r
                }\r
-\r
                try {\r
                        new Jws2Client(args);\r
                } catch (IOException e) {\r