[MOBY-guts] biomoby commit
Martin Senger
senger at pub.open-bio.org
Thu Sep 22 16:07:09 UTC 2005
senger
Thu Sep 22 12:07:08 EDT 2005
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv17235/src/Clients
Modified Files:
CacheRegistryClient.java MobyDigestClient.java
TestingCentral.java
Log Message:
moby-live/Java/src/Clients CacheRegistryClient.java,1.3,1.4 MobyDigestClient.java,1.3,1.4 TestingCentral.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2005/09/19 02:24:51 1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/CacheRegistryClient.java 2005/09/22 16:07:08 1.4
@@ -17,14 +17,14 @@
/**
* This is a command-line client creating (and removing) a cache of a
* Moby registry. It allows to store locally (in a file system)
- * objects representing data types and service instances (the service
- * types are ignored, at least for now). <p>
+ * objects representing data types, service instances, namespaces, and
+ * service types. <p>
*
* The client is quite simple and its basic functionality is included
* also in other clients (such as {@link MobyGraphs}. The reason for
* having this client separately is also to show how to use {@link
* org.biomoby.client.CentralDigestCachedImpl CentralDigestCachedImpl}
- * - a real caching worker. <p>
+ * - which is a real caching worker. <p>
*
* @author <A HREF="mailto:senger at ebi.ac.uk">Martin Senger</A>
* @version $Id$
@@ -86,40 +86,65 @@
//
// how old is the current cache?
//
- if (cmd.hasOption ("-age") || cmd.hasOption ("-rawage")) {
+ if (cmd.hasOption ("-age") || cmd.hasOption ("-rawage") || cmd.hasOption ("-agediff")) {
decorationLn ("Cache age for " + worker.getRegistryEndpoint() + ":");
long age = castWorker.getCacheAge();
if (age < 0)
- decoration ("(cache is empty)");
+ decorationLn ("(cache is empty)");
else {
if (cmd.hasOption ("-age"))
- System.out.print (new Date (castWorker.getCacheAge()).toString());
- else
- System.out.print (castWorker.getCacheAge());
+ System.out.println (new Date (age).toString());
+ if (cmd.hasOption ("-agediff"))
+ System.out.println (ms2Human (new Date().getTime() - age));
+ if (cmd.hasOption ("-ageraw"))
+ System.out.println (age);
}
- decorationLn ("");
}
//
// [re-]fill the cache
//
- if (cmd.hasOption ("-fill")) {
- castWorker.removeFromCache (null);
+ if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-d")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES);
decorationLn ("Retrieving data types...");
worker.getDataTypes();
+ }
+ if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-s")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES);
decorationLn ("Retrieving services...");
worker.getServices();
}
+ if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-t")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES);
+ decorationLn ("Retrieving service types...");
+ worker.getFullServiceTypes();
+ }
+ if (cmd.hasOption ("-fill") || cmd.hasOption ("-fill-n")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES);
+ decorationLn ("Retrieving namespaces...");
+ worker.getNamespaces();
+ }
//
// remove the cache
//
- if (cmd.hasOption ("-remove")) {
- castWorker.removeFromCache (null);
- decorationLn ("Cache removed.");
+ if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-d")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_DATATYPES);
+ decorationLn ("Cache for data types removed.");
+ }
+ if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-s")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICES);
+ decorationLn ("Cache for services removed.");
+ }
+ if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-t")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_SERVICETYPES);
+ decorationLn ("Cache for service types removed.");
+ }
+ if (cmd.hasOption ("-remove") || cmd.hasOption ("-remove-n")) {
+ castWorker.removeFromCache (CentralDigestCachedImpl.CACHE_PART_NAMESPACES);
+ decorationLn ("Cache for namespaces removed.");
}
-
} catch (Exception e) {
System.err.println ("===ERROR===");
e.printStackTrace();
@@ -128,6 +153,21 @@
}
/*************************************************************************
+ * Give me an elapsed time (given in milllis) in a human readable form.
+ *************************************************************************/
+ public static String ms2Human (long millis) {
+ StringBuffer buf = new StringBuffer (100);
+ long seconds = millis / 1000;
+ long minutes = seconds / 60;
+ long hours = minutes / 60;
+ long days = hours / 24;
+ if (days > 0)
+ buf.append (days + " days and ");
+ buf.append ((hours % 24) + ":" + (minutes % 60) + ":" + (seconds % 60) + "." + (millis % 1000));
+ return new String (buf);
+ }
+
+ /*************************************************************************
* Print 'msg' but only if in verbose mode
*************************************************************************/
static void decoration (String msg) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2005/09/19 08:08:32 1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyDigestClient.java 2005/09/22 16:07:08 1.4
@@ -67,15 +67,19 @@
if (cmd.hasOption ("-verbose"))
worker.setDebug (true);
- // read all data types and their relationships
+ // read (sometimes all) data types and their relationships
if (cmd.hasOption ("-d")) {
- MobyDataType[] dataTypes = worker.getDataTypes();
- for (int i = 0; i < dataTypes.length; i++) {
- if (details) {
+ if (details) {
+ MobyDataType[] dataTypes = worker.getDataTypes();
+ for (int i = 0; i < dataTypes.length; i++) {
System.out.println (dataTypes[i].toString());
System.out.println ("---");
- } else {
- System.out.println (dataTypes[i].getName());
+ }
+ } 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());
}
}
}
@@ -95,13 +99,21 @@
// read all services
if (cmd.hasOption ("-s")) {
- MobyService[] services = worker.getServices();
- for (int i = 0; i < services.length; i++) {
- if (details) {
+ if (details) {
+ MobyService[] services = worker.getServices();
+ for (int i = 0; i < services.length; i++) {
System.out.println (services[i].toString());
System.out.println ("---");
- } else {
- System.out.println (services[i].getName());
+ }
+ } else {
+ Map authorities = worker.getServiceNamesByAuthority();
+ for (Iterator it = authorities.entrySet().iterator(); it.hasNext(); ) {
+ Map.Entry entry = (Map.Entry)it.next();
+ String authority = (String)entry.getKey();
+ String[] names = (String[])entry.getValue();
+ for (int i = 0; i < names.length; i++) {
+ System.out.println (names[i] + " (" + authority + ")");
+ }
}
}
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2005/09/19 08:08:32 1.6
+++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2005/09/22 16:07:08 1.7
@@ -162,37 +162,35 @@
worker.setDebug (debug);
// ...and call other methods:
- String result;
-
-
+
// retrieve things
try {
start ("retrieveServiceNames");
- Map serviceNames = worker.getServiceNames();
+ worker.getServiceNamesByAuthority();
ok();
} catch (MobyException e) { error (e); }
try {
start ("retrieveServiceProviders");
- String[] providers = worker.getProviders();
+ worker.getProviders();
ok();
} catch (MobyException e) { error (e); }
try {
start ("retrieveServiceTypes");
- Map serviceTypes = worker.getServiceNames();
+ worker.getServiceTypes();
ok();
} catch (MobyException e) { error (e); }
try {
start ("retrieveNamespaces");
- Map namespaces = worker.getNamespaces();
+ worker.getNamespaces();
ok();
} catch (MobyException e) { error (e); }
try {
start ("retrieveObjectNames");
- Map typeNames = worker.getDataTypeNames();
+ worker.getDataTypeNames();
ok();
} catch (MobyException e) { error (e); }
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