[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Sat Feb 23 13:58:32 UTC 2008
senger
Sat Feb 23 08:58:32 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv3084/src/Clients
Modified Files:
CacheRegistryClient.java MirrorRegistry.java MobyGraphs.java
MosesGenerators.java
Log Message:
Merging old registry caching (without RDF) and the new one. Big changes - more will follow.
moby-live/Java/src/Clients CacheRegistryClient.java,1.8,1.9 MirrorRegistry.java,1.2,1.3 MobyGraphs.java,1.12,1.13 MosesGenerators.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2005/11/20 12:30:51 1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2008/02/23 13:58:32 1.9
@@ -7,7 +7,10 @@
//
import org.biomoby.shared.*;
-import org.biomoby.client.*;
+import org.biomoby.shared.CentralCached;
+
+import org.biomoby.client.CmdLineHelper;
+import org.biomoby.client.CentralDigestCachedImpl;
import org.biomoby.shared.event.LogListener;
import org.biomoby.shared.event.Notifier;
@@ -32,24 +35,10 @@
* @version $Id$
*/
-public class CacheRegistryClient {
-
- /*************************************************************************
- * Return a help text how to use this client.
- *************************************************************************/
- public static String getUsage() {
- String helpFile = "help/CacheRegistryClient_usage.txt";
- try {
- return new String (FileUtils.findAndGetBinaryFile (helpFile));
- } catch (GException e) {
- return
- "Sorry but an error occured.\n" +
- "I cannot find the help file '" + helpFile + "'.\n" +
- e.getMessage();
- }
- }
+public class CacheRegistryClient
+ extends CmdLineHelper {
- static boolean verbose;
+ static boolean moreVerbose = false;
/*************************************************************************
*
@@ -59,55 +48,43 @@
public static void main (String [] args) {
try {
- BaseCmdLine cmd = new BaseCmdLine (args, true);
- if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) {
- System.out.print (CacheRegistryClient.getUsage());
- System.exit (0);
- }
+ BaseCmdLine cmd = getCmdLine (args, CacheRegistryClient.class);
+
+ // where is a Moby registry
+ CentralCached worker = getCachableRegistryWorker (cmd);
// there is not much to do without -cachedir
String cacheDir = cmd.getParam ("-cachedir");
if (cacheDir == null) {
- System.err.println ("Parameter -cachedir must be specified.");
- System.exit (1);
+ emsgln ("Parameter -cachedir must be specified.");
+ exit (1);
}
-
- // where is a Moby registry
- CentralAll worker =
- new CentralDigestCachedImpl (cmd.getParam ("-e"),
- cmd.getParam ("-uri"),
- cacheDir);
- CentralDigestCachedImpl castWorker = (CentralDigestCachedImpl)worker;
// how much to show
- verbose = cmd.hasOption ("-v");
+ moreVerbose = cmd.hasOption ("-v");
if (! cmd.hasOption ("-q"))
- ((Notifier)castWorker).addNotificationListener (new LogListener());
-
- if (cmd.hasOption ("-debug")) {
- worker.setDebug (true);
- }
+ worker.addNotificationListener (new LogListener());
//
// [re-]fill the cache
//
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES);
+ worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
decorationLn ("Retrieving data types...");
worker.getDataTypes();
}
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES);
+ worker.removeFromCache (CentralCached.CACHE_PART_SERVICES);
decorationLn ("Retrieving services...");
worker.getServices();
}
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES);
+ worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
decorationLn ("Retrieving service types...");
worker.getFullServiceTypes();
}
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES);
+ worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
decorationLn ("Retrieving namespaces...");
worker.getFullNamespaces();
}
@@ -117,38 +94,38 @@
//
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) {
decorationLn ("Updating data types...");
- castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES);
+ worker.updateCache (CentralCached.CACHE_PART_DATATYPES);
}
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) {
decorationLn ("Updating services...");
- castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICES);
+ worker.updateCache (CentralCached.CACHE_PART_SERVICES);
}
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) {
decorationLn ("Updating service types...");
- castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES);
+ worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES);
}
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
decorationLn ("Updating namespaces...");
- castWorker.updateCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES);
+ worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
}
//
// remove the cache
//
if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES);
+ worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
decorationLn ("Cache for data types removed.");
}
if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-s")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES);
+ worker.removeFromCache (CentralCached.CACHE_PART_SERVICES);
decorationLn ("Cache for services removed.");
}
if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-t")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES);
+ worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
decorationLn ("Cache for service types removed.");
}
if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
- castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES);
+ worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
decorationLn ("Cache for namespaces removed.");
}
@@ -157,40 +134,37 @@
//
if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) {
decorationLn ("Cache for data types...");
- System.out.println
- (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_DATATYPES));
+ msgln
+ (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_DATATYPES));
}
if (cmd.hasOption ("-info") || cmd.hasOption ("-info-s")) {
decorationLn ("Cache for service authorities...");
- System.out.println
- (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICES));
+ msgln
+ (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICES));
}
if (cmd.hasOption ("-info") || cmd.hasOption ("-info-t")) {
decorationLn ("Cache for service types...");
- System.out.println
- (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES));
+ msgln
+ (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES));
}
if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
decorationLn ("Cache for namespaces...");
- System.out.println
- (castWorker.getCacheInfoFormatted (CentralDigestCachedImpl.CACHE_PART_NAMESPACES));
+ msgln
+ (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
}
- } catch (Exception e) {
- System.err.println ("===ERROR===");
- e.printStackTrace();
- System.err.println ("===========");
+ } catch (Throwable e) {
+ processErrorAndExit (e);
}
}
/*************************************************************************
- * Print 'msg' but only if in verbose mode
+ * Print 'msg' but only if in "more verbose" mode.
*************************************************************************/
static void decoration (String msg) {
- if (verbose) System.out.print (msg);
+ if (moreVerbose) msg (msg);
}
static void decorationLn (String msg) {
- if (verbose) System.out.println (msg);
+ if (moreVerbose) msgln (msg);
}
-
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2005/12/20 20:00:41 1.2
+++ /home/repository/moby/moby-live/Java/src/Clients/MirrorRegistry.java 2008/02/23 13:58:32 1.3
@@ -7,7 +7,9 @@
//
import org.biomoby.shared.*;
-import org.biomoby.client.*;
+import org.biomoby.client.CmdLineHelper;
+import org.biomoby.client.CentralImpl;
+import org.biomoby.shared.Central;
import org.tulsoft.tools.BaseCmdLine;
import org.tulsoft.shared.FileUtils;
@@ -23,24 +25,8 @@
* @version $Id$
*/
-public class MirrorRegistry {
-
- /*************************************************************************
- * Return a help text how to use this client.
- *************************************************************************/
- public static String getUsage() {
- String helpFile = "help/MirrorRegistry_usage.txt";
- try {
- return new String (FileUtils.findAndGetBinaryFile (helpFile));
- } catch (GException e) {
- return
- "Sorry but an error occured.\n" +
- "I cannot find the help file '" + helpFile + "'.\n" +
- e.getMessage();
- }
- }
-
- static boolean verbose;
+public class MirrorRegistry
+ extends CmdLineHelper {
/*************************************************************************
*
@@ -50,11 +36,7 @@
public static void main (String [] args) {
try {
- BaseCmdLine cmd = new BaseCmdLine (args, true);
- if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) {
- System.out.print (CacheRegistryClient.getUsage());
- System.exit (0);
- }
+ BaseCmdLine cmd = getCmdLine (args, MirrorRegistry.class);
// where are Moby registries
String eTo = cmd.getParam ("-eTo");
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/22 09:37:38 1.12
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyGraphs.java 2008/02/23 13:58:32 1.13
@@ -6,7 +6,7 @@
//
import org.biomoby.shared.*;
-import org.biomoby.shared.CentralAll;
+import org.biomoby.shared.CentralCached;
import org.biomoby.client.CmdLineHelper;
import org.biomoby.client.CentralDigestCachedImpl;
@@ -49,7 +49,7 @@
String param;
// where is a Moby registry
- CentralAll worker = getCachableRegistryWorker (cmd);
+ CentralCached worker = getCachableRegistryWorker (cmd);
// collect properties customizing graphs
Properties props = new Properties();
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/22 09:37:38 1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/MosesGenerators.java 2008/02/23 13:58:32 1.4
@@ -11,6 +11,7 @@
import org.biomoby.service.generator.ServicesGenerator;
import org.biomoby.service.generator.Generator;
import org.biomoby.shared.Central;
+import org.biomoby.shared.CentralCached;
import org.tulsoft.tools.BaseCmdLine;
import java.util.Properties;
@@ -49,10 +50,7 @@
try {
BaseCmdLine cmd = getCmdLine (args, MosesGenerators.class);
-
- Central worker = getRegistryWorker (cmd);
- String registryEndpoint = worker.getRegistryEndpoint();
- String registryNamespace = worker.getRegistryNamespace();
+ CentralCached worker = getCachableRegistryWorker (cmd);
boolean generateDataTypes = cmd.hasOption ("-dt");
boolean generateServices = cmd.hasOption ("-s");
@@ -77,8 +75,7 @@
else
qmsgln ("Generating data types" +
(outdir == null ? "..." : " into '" + outdir + "'... "));
- DataTypesGenerator dtg
- = new DataTypesGenerator (registryEndpoint, registryNamespace, cacheDir);
+ DataTypesGenerator dtg = new DataTypesGenerator (worker);
Properties props = new Properties();
if (filter != null) props.put (Generator.GPROP_FILTER, filter);
if (outdir != null) props.put (Generator.GPROP_OUTDIR, outdir);
@@ -101,8 +98,7 @@
else
qmsgln ("Generating services" +
(outdir == null ? "..." : " into '" + outdir + "'... "));
- ServicesGenerator sg
- = new ServicesGenerator (registryEndpoint, registryNamespace, cacheDir);
+ ServicesGenerator sg = new ServicesGenerator (worker);
Properties props = new Properties();
if (service != null) props.put (Generator.GPROP_SERVICE, service);
if (authority != null) props.put (Generator.GPROP_AUTH, authority);
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