[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Sun Mar 2 12:45:25 UTC 2008
senger
Sun Mar 2 07:45:25 EST 2008
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv32345/src/Clients
Modified Files:
CacheRegistryClient.java MobyDigestClient.java
TestingCentral.java
Log Message:
Too Many Changes - see docs/ChangeLog
moby-live/Java/src/Clients CacheRegistryClient.java,1.9,1.10 MobyDigestClient.java,1.8,1.9 TestingCentral.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2008/02/23 13:58:32 1.9
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2008/03/02 12:45:25 1.10
@@ -16,8 +16,7 @@
import org.biomoby.shared.event.Notifier;
import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
+import org.apache.commons.lang.time.DurationFormatUtils;
/**
* This is a command-line client creating (and removing) a cache of a
@@ -65,53 +64,91 @@
if (! cmd.hasOption ("-q"))
worker.addNotificationListener (new LogListener());
+ long started, elapsed, total = 0;
+
//
// [re-]fill the cache
//
+ if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
+ worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+ decoration ("Retrieving namespaces... ");
+ started = System.currentTimeMillis();
+ worker.getFullNamespaces();
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+ }
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) {
worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
- decorationLn ("Retrieving data types...");
+ decoration ("Retrieving data types... ");
+ started = System.currentTimeMillis();
worker.getDataTypes();
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) {
worker.removeFromCache (CentralCached.CACHE_PART_SERVICES);
- decorationLn ("Retrieving services...");
+ decoration ("Retrieving services... ");
+ started = System.currentTimeMillis();
worker.getServices();
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) {
worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
- decorationLn ("Retrieving service types...");
+ decoration ("Retrieving service types... ");
+ started = System.currentTimeMillis();
worker.getFullServiceTypes();
- }
- if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
- worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
- decorationLn ("Retrieving namespaces...");
- worker.getFullNamespaces();
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
//
// update the cache
//
+ if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
+ decoration ("Updating namespaces... ");
+ started = System.currentTimeMillis();
+ worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
+ }
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-d")) {
- decorationLn ("Updating data types...");
+ decoration ("Updating data types... ");
+ started = System.currentTimeMillis();
worker.updateCache (CentralCached.CACHE_PART_DATATYPES);
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-s")) {
- decorationLn ("Updating services...");
+ decoration ("Updating services... ");
+ started = System.currentTimeMillis();
worker.updateCache (CentralCached.CACHE_PART_SERVICES);
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
if (cmd.hasOption ("-update") || cmd.hasOption ("-update-t")) {
- decorationLn ("Updating service types...");
+ decoration ("Updating service types... ");
+ started = System.currentTimeMillis();
worker.updateCache (CentralCached.CACHE_PART_SERVICETYPES);
- }
- if (cmd.hasOption ("-update") || cmd.hasOption ("-update-n")) {
- decorationLn ("Updating namespaces...");
- worker.updateCache (CentralCached.CACHE_PART_NAMESPACES);
+ elapsed = System.currentTimeMillis() - started;
+ total += elapsed;
+ decorationLn (DurationFormatUtils.formatDurationHMS (elapsed));
}
//
// remove the cache
//
+ if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
+ worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
+ decorationLn ("Cache for namespaces removed.");
+ }
if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) {
worker.removeFromCache (CentralCached.CACHE_PART_DATATYPES);
decorationLn ("Cache for data types removed.");
@@ -124,14 +161,15 @@
worker.removeFromCache (CentralCached.CACHE_PART_SERVICETYPES);
decorationLn ("Cache for service types removed.");
}
- if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
- worker.removeFromCache (CentralCached.CACHE_PART_NAMESPACES);
- decorationLn ("Cache for namespaces removed.");
- }
//
// cache info
//
+ if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
+ decorationLn ("Cache for namespaces...");
+ msgln
+ (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
+ }
if (cmd.hasOption ("-info") || cmd.hasOption ("-info-d")) {
decorationLn ("Cache for data types...");
msgln
@@ -147,11 +185,11 @@
msgln
(worker.getCacheInfoFormatted (CentralCached.CACHE_PART_SERVICETYPES));
}
- if (cmd.hasOption ("-info") || cmd.hasOption ("-info-n")) {
- decorationLn ("Cache for namespaces...");
- msgln
- (worker.getCacheInfoFormatted (CentralCached.CACHE_PART_NAMESPACES));
- }
+
+
+ decorationLn ("Total spent time: " +
+ DurationFormatUtils.formatDurationHMS (total));
+
} catch (Throwable e) {
processErrorAndExit (e);
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2006/02/08 17:24:13 1.8
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2008/03/02 12:45:25 1.9
@@ -6,16 +6,21 @@
// Copyright Martin Senger (martin.senger at gmail.com).
//
-import org.biomoby.shared.*;
+import org.biomoby.client.CmdLineHelper;
+import org.biomoby.shared.CentralCached;
+import org.biomoby.shared.MobyDataType;
+import org.biomoby.shared.MobyNamespace;
+import org.biomoby.shared.MobyService;
+import org.biomoby.shared.MobyServiceType;
+import org.biomoby.shared.MobyData;
+import org.biomoby.shared.MobySecondaryData;
+import org.biomoby.shared.MobyPrimaryDataSet;
import org.biomoby.shared.event.SimpleListener;
-import org.biomoby.shared.event.Notifier;
-import org.biomoby.client.*;
import org.tulsoft.tools.BaseCmdLine;
-import org.tulsoft.shared.FileUtils;
-import org.tulsoft.shared.GException;
import java.util.Map;
+import java.util.Set;
import java.util.HashSet;
import java.util.Iterator;
@@ -28,22 +33,8 @@
* @version $Id$
*/
-public class MobyDigestClient {
-
- /*************************************************************************
- * Return a help text how to use this client.
- *************************************************************************/
- public static String getUsage() {
- String helpFile = "help/MobyDigest_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 MobyDigestClient
+ extends CmdLineHelper {
/*************************************************************************
*
@@ -53,38 +44,31 @@
public static void main (String [] args) {
try {
- BaseCmdLine cmd = new BaseCmdLine (args, true);
- if (cmd.hasParam ("-help") || cmd.hasParam ("-h")) {
- System.out.print (MobyDigestClient.getUsage());
- System.exit (0);
- }
+ BaseCmdLine cmd = getCmdLine (args, MobyDigestClient.class);
// where is a Moby registry
- CentralAll worker =
- new CentralDigestCachedImpl (cmd.getParam ("-e"),
- cmd.getParam ("-uri"),
- cmd.getParam ("-cachedir"));
+ CentralCached worker = getCachableRegistryWorker (cmd);
// how much to show
boolean details = cmd.hasOption ("-details");
boolean summary = cmd.hasOption ("-summary");
boolean verbose = (cmd.hasOption ("-v") || cmd.hasOption ("-verbose"));
if (verbose)
- ((Notifier)worker).addNotificationListener (new SimpleListener());
+ worker.addNotificationListener (new SimpleListener());
// read (sometimes all) data types and their relationships
if (cmd.hasOption ("-d")) {
if (details) {
MobyDataType[] dataTypes = worker.getDataTypes();
for (int i = 0; i < dataTypes.length; i++) {
- System.out.println (dataTypes[i].toString());
- System.out.println ("---");
+ msgln (dataTypes[i].toString());
+ msgln ("---");
}
} else {
Map dataTypeNames = worker.getDataTypeNames();
for (Iterator it = dataTypeNames.entrySet().iterator(); it.hasNext(); ) {
Map.Entry entry = (Map.Entry)it.next();
- System.out.println (entry.getKey());
+ msgln (entry.getKey());
}
}
}
@@ -94,9 +78,9 @@
MobyServiceType[] serviceTypes = worker.getFullServiceTypes();
for (int i = 0; i < serviceTypes.length; i++) {
if (details)
- System.out.println (serviceTypes[i]);
+ msgln (serviceTypes[i]);
else
- System.out.println (serviceTypes[i].getName());
+ msgln (serviceTypes[i].getName());
}
}
@@ -106,21 +90,21 @@
MobyService[] services = worker.getServices();
if (details) {
for (int i = 0; i < services.length; i++) {
- System.out.println (services[i]);
- System.out.println ("---");
+ msgln (services[i]);
+ msgln ("---");
}
} else { // summary
- System.out.println
+ msgln
("#Prim\t#Sec\tSType\t#Out\tInColl\tOutColl\tService\tAuthority");
for (int i = 0; i < services.length; i++) {
MobyService service = services[i];
MobyData[] pInputs = service.getPrimaryInputs();
MobyData[] sInputs = service.getSecondaryInputs();
MobyData[] outputs = service.getPrimaryOutputs();
- System.out.print (pInputs.length + "\t");
- System.out.print (sInputs.length + "\t");
+ msg (pInputs.length + "\t");
+ msg (sInputs.length + "\t");
StringBuffer buf = new StringBuffer();
- HashSet set = new HashSet();
+ Set<String> set = new HashSet<String>();
for (int j = 0; j < sInputs.length; j++) {
String abbrev =
( ((MobySecondaryData)sInputs[j]).getDataType()
@@ -130,8 +114,8 @@
set.add (abbrev);
}
}
- System.out.print (buf + "\t");
- System.out.print (outputs.length + "\t");
+ msg (buf + "\t");
+ msg (outputs.length + "\t");
boolean found = false;
for (int j = 0; j < pInputs.length; j++) {
if (pInputs[j] instanceof MobyPrimaryDataSet) {
@@ -139,7 +123,7 @@
break;
}
}
- System.out.print (found + "\t");
+ msg (found + "\t");
found = false;
for (int j = 0; j < outputs.length; j++) {
if (outputs[j] instanceof MobyPrimaryDataSet) {
@@ -147,10 +131,9 @@
break;
}
}
- System.out.print (found + "\t");
- System.out.print (service.getName() + "\t");
- System.out.print (service.getAuthority());
- System.out.println();
+ msg (found + "\t");
+ msg (service.getName() + "\t");
+ msgln (service.getAuthority());
}
}
} else {
@@ -160,7 +143,7 @@
String authority = (String)entry.getKey();
String[] names = (String[])entry.getValue();
for (int i = 0; i < names.length; i++) {
- System.out.println (names[i] + " (" + authority + ")");
+ msgln (names[i] + " (" + authority + ")");
}
}
}
@@ -171,16 +154,14 @@
MobyNamespace[] namespaces = worker.getFullNamespaces();
for (int i = 0; i < namespaces.length; i++) {
if (details)
- System.out.println (namespaces[i]);
+ msgln (namespaces[i]);
else
- System.out.println (namespaces[i].getName());
+ msgln (namespaces[i].getName());
}
}
- } catch (Exception e) {
- System.err.println ("===ERROR===");
- e.printStackTrace();
- System.err.println ("===========");
+ } catch (Throwable e) {
+ processErrorAndExit (e);
}
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2006/12/07 18:41:00 1.10
+++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2008/03/02 12:45:25 1.11
@@ -94,8 +94,8 @@
}
if (type.equalsIgnoreCase ("Integer")) {
data.setDefaultValue ("123");
- data.setMaximumValue (234);
- data.setMinimumValue (23);
+ data.setMaxValue ("234");
+ data.setMinValue ("23");
data.addAllowedValue ("30");
data.addAllowedValue ("40");
data.addAllowedValue ("50");
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