[MOBY-guts] biomoby commit

Martin Senger senger at pub.open-bio.org
Sun Sep 4 13:45:37 UTC 2005


senger
Sun Sep  4 09:45:37 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv27838/src/Clients

Modified Files:
	CacheRegistryClient.java MobyCmdLineClient.java 
	MobyDigestClient.java MobyGraphs.java MosesGenerators.java 
	TestArgs.java TestingMobyParser.java 
	UnregisterByAuthority.java 
Log Message:


moby-live/Java/src/Clients CacheRegistryClient.java,1.1,1.2 MobyCmdLineClient.java,1.10,1.11 MobyDigestClient.java,1.1,1.2 MobyGraphs.java,1.8,1.9 MosesGenerators.java,1.1,1.2 TestArgs.java,1.1,1.2 TestingMobyParser.java,1.1,1.2 UnregisterByAuthority.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2004/11/14 16:12:50	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java	2005/09/04 13:45:37	1.2
@@ -8,8 +8,9 @@
 import org.biomoby.shared.*;
 import org.biomoby.client.*;
 
-import embl.ebi.tools.*;
-import embl.ebi.utils.*;
+import org.tulsoft.tools.BaseCmdLine;
+import org.tulsoft.shared.FileUtils;
+import org.tulsoft.shared.GException;
 
 import java.net.*;
 import java.util.*;

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2005/08/07 06:30:49	1.10
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2005/09/04 13:45:37	1.11
@@ -8,8 +8,10 @@
 import org.biomoby.shared.*;
 import org.biomoby.client.*;
 
-import embl.ebi.tools.*;
-import embl.ebi.utils.*;
+import org.tulsoft.tools.BaseCmdLine;
+import org.tulsoft.shared.FileUtils;
+import org.tulsoft.shared.StringUtils;
+import org.tulsoft.shared.GException;
 
 import java.net.*;
 import java.util.*;
@@ -268,12 +270,12 @@
 		data.setAuthority (cmd.getParam ("-rd-auth"));
 		data.setEmailContact (cmd.getParam ("-rd-email"));
                 if ((param = cmd.getParam ("-rd-isa")) != null ) {
-		    String[] isas = StringUtils.split (param, ",");
+		    String[] isas = param.split (",");
 		    for (int i = 0; i < isas.length; i++)
 			data.addParentName (isas [i]);
 		}
                 if ((param = cmd.getParam ("-rd-hasa")) != null ) {
-		    String[] hasas = StringUtils.split (param, ",");
+		    String[] hasas = param.split (",");
 		    for (int i = 0; i < hasas.length; i++) {
 			int pos = hasas[i].indexOf (":");
 			if (pos == -1) {
@@ -286,7 +288,7 @@
 		    }
 		}
                 if ((param = cmd.getParam ("-rd-has")) != null ) {
-		    String[] hasas = StringUtils.split (param, ",");
+		    String[] hasas = param.split (",");
 		    for (int i = 0; i < hasas.length; i++) {
 			int pos = hasas[i].indexOf (":");
 			if (pos == -1) {
@@ -310,7 +312,7 @@
 		stype.setAuthority (cmd.getParam ("-rt-auth"));
 		stype.setEmailContact (cmd.getParam ("-rt-email"));
                 if ((param = cmd.getParam ("-rt-isa")) != null ) {
-		    String[] isas = StringUtils.split (param, ",");
+		    String[] isas = param.split (",");
 		    for (int i = 0; i < isas.length; i++)
 			stype.addParentName (isas [i]);
 		}
@@ -351,9 +353,9 @@
 		}
 
                 if ( (param = cmd.getParam ("-rs-in")) != null ) {
-		    String[] inputs = StringUtils.split (param, ",");
+		    String[] inputs = param.split (",");
 		    for (int i = 0; i < inputs.length; i++) {
-			String[] parts = StringUtils.split (inputs[i], "=");
+			String[] parts = inputs[i].split ("=");
 			if (parts.length >= 2) {
 			    MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy");
 			    data.setDataType (new MobyDataType (parts[0]));
@@ -367,7 +369,7 @@
 		    }
 		}
                 if ((param = cmd.getParam ("-rs-ifile")) != null ) {
-		    String[] files = StringUtils.split (param, ",");
+		    String[] files = param.split (",");
 		    for (int i = 0; i < files.length; i++) {
 			Properties props = new Properties();
 			try {
@@ -421,9 +423,9 @@
 		    }
 		}
                 if ((param = cmd.getParam ("-rs-out")) != null ) {
-		    String[] outs = StringUtils.split (param, ",");
+		    String[] outs = param.split (",");
 		    for (int i = 0; i < outs.length; i++) {
-			String[] parts = StringUtils.split (outs[i], "=");
+			String[] parts = outs[i].split ("=");
 			if (parts.length >= 2) {
 			    MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy");
 			    data.setDataType (new MobyDataType (parts[0]));
@@ -437,7 +439,7 @@
 		    }
 		}
                 if ((param = cmd.getParam ("-rs-ofile")) != null ) {
-		    String[] files = StringUtils.split (param, ",");
+		    String[] files = param.split (",");
 		    for (int i = 0; i < files.length; i++) {
 			Properties props = new Properties();
 			try {
@@ -535,7 +537,7 @@
 	    if ((param = cmd.getParam ("-f")) != null ) {
 		decorationLn ("Looking for services related to: '" + param + "':");
 		decorationLn ("--------------------------------");
-		printServices (worker.findService (StringUtils.split (param, ",")),
+		printServices (worker.findService (param.split (",")),
 			       cmd.hasOption ("-on"));
 	    }
 
@@ -555,9 +557,9 @@
 		pattern.setType (cmd.getParam ("-fs-type"));
 		pattern.setAuthority (cmd.getParam ("-fs-auth"));
                 if ((param = cmd.getParam ("-fs-in")) != null ) {
-		    String[] inputs = StringUtils.split (param, ",");
+		    String[] inputs = param.split (",");
 		    for (int i = 0; i < inputs.length; i++) {
-			String[] parts = StringUtils.split (inputs[i], "=");
+			String[] parts = inputs[i].split ("=");
 			MobyPrimaryDataSimple input = new MobyPrimaryDataSimple ("dummy");
 			input.setDataType (new MobyDataType (parts[0]));
 			if (parts.length >= 2)
@@ -566,7 +568,7 @@
 		    }
 		}
                 if ((param = cmd.getParam ("-fs-out")) != null ) {
-		    String[] outs = StringUtils.split (param, ",");
+		    String[] outs = param.split (",");
 		    for (int i = 0; i < outs.length; i++) {
 			MobyPrimaryDataSimple output = new MobyPrimaryDataSimple ("dummy");
 			output.setDataType (new MobyDataType (outs[i]));

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2004/11/14 16:43:49	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java	2005/09/04 13:45:37	1.2
@@ -7,8 +7,9 @@
 import org.biomoby.shared.*;
 import org.biomoby.client.*;
 
-import embl.ebi.tools.*;
-import embl.ebi.utils.*;
+import org.tulsoft.tools.BaseCmdLine;
+import org.tulsoft.shared.FileUtils;
+import org.tulsoft.shared.GException;
 
 /**
  * A simple client retrieving and printing cummulative (digestive)

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java	2005/07/19 12:39:58	1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java	2005/09/04 13:45:37	1.9
@@ -8,8 +8,11 @@
 import org.biomoby.shared.*;
 import org.biomoby.client.*;
 
-import embl.ebi.tools.*;
-import embl.ebi.utils.*;
+import org.tulsoft.tools.BaseCmdLine;
+import org.tulsoft.tools.Printf;
+import org.tulsoft.shared.UUtils;
+import org.tulsoft.shared.FileUtils;
+import org.tulsoft.shared.GException;
 
 import java.net.*;
 import java.util.*;
@@ -146,7 +149,7 @@
 		    while ((line = data.readLine()) != null) {
 			if (line.trim().equals ("")) continue;
 			if (line.trim().startsWith ("#")) continue;
-			String[] fields = StringUtils.split (line);
+			String[] fields = line.split ("\\s+");
 			if (fields.length > 1) {
 			    if (fields[0].equalsIgnoreCase ("start")) {
 				DataServiceEdge dse = new DataServiceEdge (new MobyDataType ("start"),
@@ -181,9 +184,9 @@
 		String[] serviceNames = null;
 		int depth = 1;
                 if ((param = cmd.getParam ("-auth")) != null )
-		    authorities = StringUtils.split (param, ",");
+		    authorities = param.split (",");
                 if ((param = cmd.getParam ("-name")) != null )
-		    serviceNames = StringUtils.split (param, ",");
+		    serviceNames = param.split (",");
 		param = cmd.getParam ("-depth");
 		if (param != null) {
 		    try {

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2005/08/26 06:27:03	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java	2005/09/04 13:45:37	1.2
@@ -12,7 +12,7 @@
 import org.biomoby.shared.MobyException;
 import org.biomoby.shared.Utils;
 
-import embl.ebi.tools.BaseCmdLine;
+import org.tulsoft.tools.BaseCmdLine;
 import java.util.Properties;
 
 /**

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestArgs.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/TestArgs.java	2005/09/01 05:51:18	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/TestArgs.java	2005/09/04 13:45:37	1.2
@@ -6,6 +6,9 @@
 // Copyright Martin Senger (martin.senger at gmail.com).
 //
 
+import org.tulsoft.tools.BaseCmdLine;
+import org.tulsoft.shared.UUtils;
+
 /**
  * Work in progress...
  *
@@ -16,8 +19,17 @@
 
     public static void main (String[] args)
 	throws Exception {
-	for (int i = 0; i < args.length; i++) {
-	    System. out.println (i + ": " + args[i]);
+	String withTools = System.getProperty ("with_tools");
+	if (UUtils.is (withTools)) {
+	    System.out.println ("Using BaseCmdLine:\n");
+	    BaseCmdLine cmd = new BaseCmdLine (args, true);
+	    for (int i = 0; i < cmd.params.length; i++) {
+		System. out.println (i + ": " + cmd.params[i]);
+	    }
+	} else {
+	    for (int i = 0; i < args.length; i++) {
+		System. out.println (i + ": " + args[i]);
+	    }
 	}
     }
 }

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java	2005/08/26 06:27:03	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/TestingMobyParser.java	2005/09/04 13:45:37	1.2
@@ -10,7 +10,7 @@
 import org.biomoby.shared.MobyException;
 import org.biomoby.shared.Utils;
 
-import embl.ebi.tools.BaseCmdLine;
+import org.tulsoft.tools.BaseCmdLine;
 import java.io.File;
 
 /**

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java	2005/08/26 06:27:03	1.1
+++ /home/repository/moby/moby-live/Java/src/Clients/UnregisterByAuthority.java	2005/09/04 13:45:37	1.2
@@ -11,7 +11,7 @@
 import org.biomoby.shared.Central;
 import org.biomoby.client.CentralImpl;
 
-import embl.ebi.tools.BaseCmdLine;
+import org.tulsoft.tools.BaseCmdLine;
 
 import java.util.Map;
 import java.util.Map.Entry;




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