From gordonp at dev.open-bio.org Wed Nov 1 18:44:34 2006
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 1 Nov 2006 18:44:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611012344.kA1NiYbF000888@dev.open-bio.org>
gordonp
Wed Nov 1 18:44:34 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui
In directory dev.open-bio.org:/tmp/cvs-serv853/src/main/ca/ucalgary/seahawk/gui
Modified Files:
MobyServicesGUI.java
Log Message:
Multiline the input data type tooltip, rather than truncate it
moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyServicesGUI.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2006/10/27 20:55:14 1.5
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyServicesGUI.java 2006/11/01 23:44:34 1.6
@@ -1214,8 +1214,11 @@
submenu = new JMenu("Services for " + objectLabel);
assignMenuDataIndex(submenu);
}
-
- submenu.setToolTipText("Input data: " + desc);
+ desc = "Input data: " + desc;
+ if(desc.length() > MAX_SERVICE_DESC_LEN){
+ desc = htmlifyToolTipText(desc);
+ }
+ submenu.setToolTipText(desc);
submenu.setName(SERVICE_SUBMENU_NAME);
return submenu;
}
From gordonp at dev.open-bio.org Wed Nov 1 18:45:36 2006
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 1 Nov 2006 18:45:36 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611012345.kA1Nja4P000931@dev.open-bio.org>
gordonp
Wed Nov 1 18:45:36 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv896/src/main/ca/ucalgary/seahawk/util
Modified Files:
MinJarMaker.java
Log Message:
Changes to allow the ClassLoader to extract classes from JARs in the minnow classpath variable
moby-live/Java/src/main/ca/ucalgary/seahawk/util MinJarMaker.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/10/30 15:56:19 1.1
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/11/01 23:45:36 1.2
@@ -45,7 +45,7 @@
// For the class loading interface, keep track of what we've loaded
private Set loadedClasses =
- Collections.synchronizedSet( new HashSet() );
+ Collections.synchronizedSet( new LinkedHashSet() );
static public void main( String args[] ) throws Exception {
// Check arguments
@@ -254,6 +254,11 @@
}
static protected String truncateURL(URL fullURL){
+ int jarSpecIndex = fullURL.toString().indexOf("!/");
+ if(jarSpecIndex != -1){
+ return fullURL.toString().substring(jarSpecIndex+2);
+ }
+
StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"), File.pathSeparator);
while(classPathTokens.hasMoreElements()){
String classPathElement = classPathTokens.nextToken();
@@ -273,49 +278,86 @@
return null;
}
- protected String classToPath( String name ) {
+ protected byte[] getClassBytes( String name ) throws IOException {
// Check all of the run-time specified class path dirs for the
// class file in question
- StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"), File.pathSeparator);
+ StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"),
+ File.pathSeparator);
while(classPathTokens.hasMoreElements()){
- String path = classPathTokens.nextToken() + File.separator + name.replace( '.', File.separatorChar);
- path += ".class";
+ String pathElement = classPathTokens.nextToken();
+ // Turn package.class name into a relative path of a class resource
+ String pathSuffix = name.replace('.', File.separatorChar) + ".class";
+ String path = pathElement + File.separator + pathSuffix;
File classFile = new File(path);
- if(classFile.exists()){
- return path;
+ if(classFile.isFile()){
+ long len = classFile.length();
+ byte data[] = new byte[(int)len];
+ FileInputStream fin = new FileInputStream(classFile);
+ int r = fin.read(data);
+ if (r != len){
+ throw new IOException( "Could only read "+r+" of "+len+" bytes from "+classFile );
+ }
+ fin.close();
+ return data;
+ }
+ else{
+ // If it's not a file, maybe it's in a JAR
+ File f = new File(pathElement);
+ if(f.isFile()){
+ JarFile jarFile = null;
+ try{
+ jarFile = new JarFile(f);
+ }
+ catch(Exception e){
+ System.err.println("Class path element " + pathElement +
+ " was not a directory, or a valid JAR file");
+ continue;
+ }
+
+ JarEntry je = jarFile.getJarEntry(pathSuffix);
+ if(je == null){
+ continue;
+ }
+ long classSize = je.getSize();
+
+ InputStream classStream = jarFile.getInputStream(je);
+ byte[] classBytes = null;
+ if(classSize != -1){ // We know the size of the class already
+
+ classBytes = new byte[(int) classSize]; //classes better not be bigger than 2 GB!
+ // Slurp it up in one shot
+ classStream.read(classBytes, 0, (int) classSize);
+ return classBytes;
+ }
+ else{
+
+ byte[] byteBufferChunk = new byte[1024];
+ ByteArrayOutputStream byteBuffer = new ByteArrayOutputStream();
+ for(int r = classStream.read(byteBufferChunk, 0, 1024);
+ r != -1;
+ r = classStream.read(byteBufferChunk, 0, 1024)){
+ byteBuffer.write(byteBufferChunk, 0, r);
+ }
+ return byteBuffer.toByteArray();
+ }
+ }
+
}
}
return null;
}
- protected byte[] readFile( String filename ) throws IOException {
- File file = new File( filename );
- long len = file.length();
- byte data[] = new byte[(int)len];
- FileInputStream fin = new FileInputStream( file );
- int r = fin.read( data );
- if (r != len)
- throw new IOException( "Could only read "+r+" of "+len+" bytes from "+file );
- fin.close();
- return data;
- }
-
- protected byte[] getClassBytes( String name ) throws IOException {
- String path = classToPath( name );
- if(path == null)
- return null;
- return readFile( path );
- }
-
- protected URL getResourceURL(String name){
+ protected URL getResourceURL(String name){
// Check all of the run-time specified class path dirs for the
// properties file in question
- StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"), File.pathSeparator);
+ StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"),
+ File.pathSeparator);
while(classPathTokens.hasMoreElements()){
- String path = classPathTokens.nextToken() + File.separator + name;
+ String pathElement = classPathTokens.nextToken();
+ String path = pathElement + File.separator + name;
File resourceFile = new File(path);
- if(resourceFile.exists()){
+ if(resourceFile.isFile()){
try{
return resourceFile.toURL();
}
@@ -324,6 +366,43 @@
path + " as URL, but could not: " + e);
}
}
+ else{
+ // If it's not a file, maybe it's in a JAR
+ File f = new File(pathElement);
+ if(f.isFile()){
+ JarFile jarFile = null;
+ try{
+ jarFile = new JarFile(f);
+ }
+ catch(Exception e){
+ System.err.println("Class path element " + pathElement +
+ " was not a directory, or a valid JAR file");
+ continue;
+ }
+
+ JarEntry je = jarFile.getJarEntry(name);
+ try{
+ jarFile.close();
+ }
+ catch(IOException ioe){
+ System.err.println("Couldn't close JAR file: " + pathElement);
+ }
+ if(je == null){
+ continue;
+ }
+ else{
+ try{
+ return new URL("jar:"+f.toURL().toString()+"!/"+name);
+ } catch(java.net.MalformedURLException murle){
+ try{
+ System.err.println("URL jar:"+f.toURL().toString()+"!"+name +
+ " was invalid: " +murle);}catch(Exception e){}
+ return null;
+ }
+ }
+ }
+
+ }
}
return null;
}
@@ -341,6 +420,11 @@
}
}
+ protected void copyFile( OutputStream out, byte[] buffer )
+ throws IOException {
+ out.write(buffer);
+ }
+
protected void copyFile( OutputStream out, String infile )
throws IOException {
FileInputStream fin = new FileInputStream( infile );
@@ -400,11 +484,11 @@
}
}
- // Store the class
- String path = classToPath( classname );
+ // Store the class, TODO: be updated since JAR class origins allowed
+ byte[] classBytes = getClassBytes(classname);
String relativePath = null;
- if(path != null){ // Found it
- relativePath = truncatePath(path);
+ if(classBytes != null){ // Found it
+ relativePath = classname.replaceAll("\\.", File.separator)+".class";
if(savedClasses.containsKey(relativePath)){
continue; //already saved
}
@@ -412,14 +496,18 @@
//System.out.println( "Adding class "+path );
JarEntry je = new JarEntry(relativePath);
jout.putNextEntry( je );
- copyFile( jout, path );
+ copyFile(jout, classBytes);
jout.closeEntry();
}
else { // A resource, not a class?
java.net.URL resourceURL = getResourceURL(classname);
if(resourceURL != null){
relativePath = truncateURL(resourceURL);
- if(savedClasses.containsKey(relativePath)){
+ if(relativePath == null){
+ System.err.println("Could not create relative path for "+ resourceURL + ", excluding from JAR");
+ continue;
+ }
+ else if(savedClasses.containsKey(relativePath)){
continue; //already saved
}
@@ -430,7 +518,7 @@
jout.closeEntry();
}
else{
- System.err.println("Warning: Could not find class or resource file for " + classname);
+ System.err.println("Warning: Could not find class or resource file for " + classname + ", excluding from JAR" );
continue;
}
}
From gordonp at dev.open-bio.org Wed Nov 1 18:46:59 2006
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 1 Nov 2006 18:46:59 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611012346.kA1NkxYa001012@dev.open-bio.org>
gordonp
Wed Nov 1 18:46:59 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test
In directory dev.open-bio.org:/tmp/cvs-serv981/src/main/ca/ucalgary/seahawk/gui/test
Added Files:
moby_exception.xml allDataTypes.xml
Log Message:
File used in Seahawk unit tests
moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test moby_exception.xml,NONE,1.1 allDataTypes.xml,NONE,1.1
From senger at dev.open-bio.org Sat Nov 11 18:04:34 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 11 Nov 2006 18:04:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611112304.kABN4Yi3015153@dev.open-bio.org>
senger
Sat Nov 11 18:04:34 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv15098/src/main/org/biomoby/shared/parser
Modified Files:
ServiceException.java
Log Message:
removing java warnings + update of Perl-Moses
moby-live/Java/src/main/org/biomoby/shared/parser ServiceException.java,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2006/10/25 02:33:23 1.10
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/parser/ServiceException.java 2006/11/11 23:04:34 1.11
@@ -128,14 +128,14 @@
protected int code = OK;
protected String description;
- static HashMap severityNames = new HashMap();
+ static HashMap severityNames = new HashMap();
static {
severityNames.put (new Integer (ERROR), "error");
severityNames.put (new Integer (WARNING), "warning");
severityNames.put (new Integer (INFO), "information");
}
- static HashMap codeNames = new HashMap();
+ static HashMap codeNames = new HashMap();
static {
codeNames.put (new Integer (OK), "OK");
codeNames.put (new Integer (UNKNOWN_NAME), "UNKNOWN_NAME");
@@ -436,22 +436,23 @@
* @return an array, potentially an empty array, of all exceptions
* extracted from the 'serviceNotes'
*************************************************************************/
+ @SuppressWarnings("unchecked")
public static ServiceException[] extractExceptions (Element serviceNotes) {
if (serviceNotes == null)
return new ServiceException[] {};
- Vector v = new Vector();
- for (Iterator it =
+ Vector v = new Vector();
+ for (Iterator it =
serviceNotes.getChildren (MobyTags.MOBYEXCEPTION).iterator();
it.hasNext(); ) {
- ServiceException ex = extractException ((Element)it.next());
+ ServiceException ex = extractException (it.next());
if (ex != null)
v.addElement (ex);
}
- for (Iterator it =
+ for (Iterator it =
serviceNotes.getChildren (MobyTags.MOBYEXCEPTION, JDOMUtils.MOBY_NS).iterator();
it.hasNext(); ) {
- ServiceException ex = extractException ((Element)it.next());
+ ServiceException ex = extractException (it.next());
if (ex != null)
v.addElement (ex);
}
From senger at dev.open-bio.org Sat Nov 11 18:04:34 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 11 Nov 2006 18:04:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611112304.kABN4Yub015133@dev.open-bio.org>
senger
Sat Nov 11 18:04:34 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv15098/src/main/org/biomoby/shared
Modified Files:
MobyPrimaryDataSet.java MobyPrimaryDataSimple.java
MobySecondaryData.java MobyService.java Utils.java
Log Message:
removing java warnings + update of Perl-Moses
moby-live/Java/src/main/org/biomoby/shared MobyPrimaryDataSet.java,1.8,1.9 MobyPrimaryDataSimple.java,1.9,1.10 MobySecondaryData.java,1.8,1.9 MobyService.java,1.14,1.15 Utils.java,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSet.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSet.java 2006/10/30 15:55:36 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSet.java 2006/11/11 23:04:34 1.9
@@ -24,7 +24,8 @@
public class MobyPrimaryDataSet
extends MobyPrimaryData {
- protected Vector elements = new Vector(); // elemenst are of type MobyPrimaryDataSimple
+ protected Vector elements =
+ new Vector();
protected MobyDataType defaultDataType = new MobyDataType("Object");
/**************************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2006/07/07 04:12:40 1.9
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2006/11/11 23:04:34 1.10
@@ -28,7 +28,7 @@
public class MobyPrimaryDataSimple
extends MobyPrimaryData {
- protected Vector namespaces = new Vector(); // elements are of type MobyNamespace
+ protected Vector namespaces = new Vector();
protected MobyDataType dataType;
/**************************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java 2006/07/07 04:12:40 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobySecondaryData.java 2006/11/11 23:04:34 1.9
@@ -28,7 +28,7 @@
protected String defaultValue = "";
protected String minimumValue = "";
protected String maximumValue = "";
- protected Vector allowedValues = new Vector();
+ protected Vector allowedValues = new Vector();
protected String description = "";
/**************************************************************************
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2006/10/26 00:33:35 1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2006/11/11 23:04:34 1.15
@@ -67,9 +67,9 @@
protected static MobyService[] services = uninitializedServices;
// the elements of these Vectors are of type MobyData
- protected Vector primaryInputs = new Vector();
- protected Vector secondaryInputs = new Vector();
- protected Vector primaryOutputs = new Vector();
+ protected Vector primaryInputs = new Vector();
+ protected Vector secondaryInputs = new Vector();
+ protected Vector primaryOutputs = new Vector();
/**************************************************************************
* Implementing Comparable interface.
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2006/09/27 11:15:59 1.16
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Utils.java 2006/11/11 23:04:34 1.17
@@ -468,7 +468,7 @@
/*************************************************************************
*
*************************************************************************/
- protected static HashSet javaReserved = new HashSet();
+ protected static HashSet javaReserved = new HashSet();
static {
javaReserved.add ("abstract");
javaReserved.add ("assert");
From senger at dev.open-bio.org Sat Nov 11 18:04:34 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Sat, 11 Nov 2006 18:04:34 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611112304.kABN4Ykg015173@dev.open-bio.org>
senger
Sat Nov 11 18:04:34 EST 2006
Update of /home/repository/moby/moby-live/Java/src/scripts
In directory dev.open-bio.org:/tmp/cvs-serv15098/src/scripts
Modified Files:
install.pl
Log Message:
removing java warnings + update of Perl-Moses
moby-live/Java/src/scripts install.pl,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/scripts/install.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/scripts/install.pl 2006/10/16 18:07:15 1.6
+++ /home/repository/moby/moby-live/Java/src/scripts/install.pl 2006/11/11 23:04:34 1.7
@@ -47,6 +47,8 @@
}
}
+ use constant MSWIN => $^O =~ /MSWin32|Windows_NT/i ? 1 : 0;
+
say 'Welcome, BioMobiers. Preparing stage for Perl MoSeS...';
say '------------------------------------------------------';
@@ -59,11 +61,20 @@
Template
Config::Simple
IO::Scalar
- IO::Prompt
Unicode::String
) ) {
check_module ($module);
}
+ if (MSWIN) {
+ check_module ('Term::ReadLine');
+ {
+ local $^W = 0;
+ $SimplePrompt::Terminal = Term::ReadLine->new ('Installation');
+ }
+ } else {
+ check_module ('IO::Prompt');
+ require IO::Prompt; import IO::Prompt;
+ }
if ($errors_found) {
say "\nSorry, some needed modules were not found.";
say "Please install them and run 'install.pl' again.";
@@ -76,26 +87,31 @@
use lib "$Bin/../Perl"; # assuming: Perl/MOSES/...
# scripts/install.pl
use File::Spec;
-use IO::Prompt;
use MOSES::MOBY::Base;
use MOSES::MOBY::Cache::Central;
use MOSES::MOBY::Cache::Registries;
use English qw( -no_match_vars ) ;
use strict;
+# different prompt modules used for different OSs
+# ('pprompt' as 'proxy_prompt')
+sub pprompt {
+ return prompt (@_) unless MSWIN;
+ return SimplePrompt::prompt (@_);
+}
# $prompt ... a prompt asking for a directory
# $prompted_dir ... suggested directory
sub prompt_for_directory {
my ($prompt, $prompted_dir) = @_;
while (1) {
- my $dir = prompt ("$prompt [$prompted_dir] ");
+ my $dir = pprompt ("$prompt [$prompted_dir] ");
$dir =~ s/^\s*//; $dir =~ s/\s*$//;
$dir = $prompted_dir unless $dir;
return $dir if -d $dir and -w $dir; # okay: writable directory
$prompted_dir = $dir;
next if -e $dir and say "'$dir' is not a writable directory. Try again please.";
- next unless prompt ("Directory '$dir' does not exists. Create? ", -yn);
+ next unless pprompt ("Directory '$dir' does not exists. Create? ", -yn);
# okay, we agreed to create it
mkdir $dir and return $dir;
@@ -107,7 +123,7 @@
sub prompt_for_registry {
my $cache = new MOSES::MOBY::Cache::Central;
my @regs = MOSES::MOBY::Cache::Registries->list;
- my $registry = prompt ("What registry to use? [default] ",
+ my $registry = pprompt ("What registry to use? [default] ",
-m => [@regs]);
$registry ||= 'default';
}
@@ -144,14 +160,13 @@
# --- main ---
no warnings 'once';
-my $pmoses_home = File::Spec->catfile ($Bin, '..', 'Perl');
-my $jmoby_home = File::Spec->catfile ($Bin, '..', '..');
+my $pmoses_home = "$Bin/../Perl";
+my $jmoby_home = "$Bin/../..";
say "Installing in $pmoses_home\n";
# log files (create, or just change their write permissions)
-my $log_file1 = $MOBYCFG::LOG_FILE ||
- File::Spec->catfile ($pmoses_home, 'services.log');
-my $log_file2 = File::Spec->catfile ($pmoses_home, 'parser.log');
+my $log_file1 = $MOBYCFG::LOG_FILE || "$pmoses_home/services.log";
+my $log_file2 = "$pmoses_home/parser.log";
foreach my $file ($log_file1, $log_file2) {
unless (-e $file) {
eval {
@@ -164,15 +179,14 @@
}
# log4perl property file (will be found and used, or created)
-my $log4perl_file = $MOBYCFG::LOG_CONFIG ||
- File::Spec->catfile ($pmoses_home, 'log4perl.properties');
+my $log4perl_file = $MOBYCFG::LOG_CONFIG || "$pmoses_home/log4perl.properties";
if (-e $log4perl_file and ! $opt_F) {
say "\nLogging property file '$log4perl_file' exists.";
say "It will not be overwritten unless you start 'install.pl -F'.\n";
} else {
file_from_template
($log4perl_file,
- File::Spec->catfile ($pmoses_home, 'log4perl.properties.template'),
+ "$pmoses_home/log4perl.properties.template",
'Log properties file',
{ '@LOGFILE@' => $log_file1,
'@LOGFILE2@' => $log_file2,
@@ -181,20 +195,20 @@
# MobyServer.cgi file
my $generated_dir = $MOBYCFG::GENERATORS_OUTDIR ||
- File::Spec->catfile ($pmoses_home, 'generated');
+ "$pmoses_home/generated";
my $services_dir = $MOBYCFG::GENERATORS_IMPL_OUTDIR ||
- File::Spec->catfile ($pmoses_home, 'services');
+ "$pmoses_home/services";
my $services_table = $MOBYCFG::GENERATORS_IMPL_SERVICES_TABLE ||
'SERVICES_TABLE';
-my $cgibin_file = File::Spec->catfile ($pmoses_home, 'MobyServer.cgi');
+my $cgibin_file = "$pmoses_home/MobyServer.cgi";
if (-e $cgibin_file and ! $opt_F) {
say "\nWeb Server file '$cgibin_file' exists.";
say "It will not be overwritten unless you start 'install.pl -F'.\n";
} else {
file_from_template
($cgibin_file,
- File::Spec->catfile ($pmoses_home, 'MobyServer.cgi.template'),
+ "$pmoses_home/MobyServer.cgi.template",
'Web Server file',
{ '@PMOSES_HOME@' => $pmoses_home,
'@GENERATED_DIR@' => $generated_dir,
@@ -207,12 +221,12 @@
# directory for local cache
my $cachedir = $MOBYCFG::CACHEDIR ||
prompt_for_directory ( 'Directory for local cache',
- File::Spec->catfile ($jmoby_home, 'myCache'));
+ "$jmoby_home/myCache");
say "Local cache in '$cachedir'.\n";
# filling/updating local cache
my $registry = 'default';
-if ('y' eq prompt ('Should I try to fill or update the local cache [y]? ', -ynd=>'y')) {
+if ('y' eq pprompt ('Should I try to fill or update the local cache [y]? ', -ynd=>'y')) {
$registry = prompt_for_registry;
my $details =
MOSES::MOBY::Cache::Registries->get ($registry);
@@ -221,11 +235,10 @@
my $uri = $details->{namespace};
say 'Using registry: ' . $registry;
say "(at $endpoint)\n";
-# my $os = ($OSNAME =~ /Win/i ? '.bat' : '');
my $run_script =
File::Spec->catfile ($jmoby_home, 'build', 'run', 'run-cache-client');
if (-e $run_script) {
- my $cmd = "$run_script -e $endpoint -uri $uri -cachedir $cachedir -update";
+ my $cmd = "\"$run_script\" -e $endpoint -uri $uri -cachedir $cachedir -update";
say "The following command will be executed to update the cache:\n\n$cmd\n";
say "Updating local cache (it may take several minutes)...\n";
print `$cmd`;
@@ -248,7 +261,7 @@
} else {
file_from_template
($config_file,
- File::Spec->catfile ($pmoses_home, 'moby-services.cfg.template'),
+ "$pmoses_home/moby-services.cfg.template",
'Configuration file',
{ '@CACHE_DIR@' => $cachedir,
'@REGISTRY@' => $registry,
@@ -258,11 +271,93 @@
'@LOG4PERL_FILE@' => $log4perl_file,
'@LOGFILE@' => $log_file1,
'@MABUHAY_RESOURCE@' =>
- File::Spec->catfile ($jmoby_home, 'src', 'samples-resources', 'mabuhay.file'),
+ "$jmoby_home/src/samples-resources/mabuhay.file",
} );
}
say 'Done.';
+package SimplePrompt;
+
+use vars qw/ $Terminal /;
+
+sub prompt {
+ my ($msg, $flags, $others) = @_;
+
+ # simple prompt
+ return get_input ($msg)
+ unless $flags;
+
+ $flags =~ s/^-//o; # ignore leading dash
+
+ # 'waiting for yes/no' prompt, possibly with a default value
+ if ($flags =~ /^yn(d)?/i) {
+ return yes_no ($msg, $others);
+ }
+
+ # prompt with a menu of possible answers
+ if ($flags =~ /^m/i) {
+ return menu ($msg, $others);
+ }
+
+ # default: again a simple prompt
+ return get_input ($msg);
+}
+
+sub yes_no {
+ my ($msg, $default_answer) = @_;
+ while (1) {
+ my $answer = get_input ($msg);
+ return $default_answer if $default_answer and $answer =~ /^\s*$/o;
+ return 'y' if $answer =~ /^(1|y|yes|ano)$/;
+ return 'n' if $answer =~ /^(0|n|no|ne)$/;
+ }
+}
+
+sub get_input {
+ my ($msg) = @_;
+ local $^W = 0;
+ my $line = $Terminal->readline ($msg);
+ chomp $line; # remove newline
+ $line =~ s/^\s*//; $line =~ s/\s*$//; # trim whitespaces
+ $Terminal->addhistory ($line) if $line;
+ return $line;
+}
+
+sub menu {
+ my ($msg, $ra_menu) = @_;
+ my @data = @$ra_menu;
+
+ my $count = @data;
+# die "Too many -menu items" if $count > 26;
+# die "Too few -menu items" if $count < 1;
+
+ my $max_char = chr(ord('a') + $count - 1);
+ my $menu = '';
+
+ my $next = 'a';
+ foreach my $item (@data) {
+ $menu .= ' ' . $next++ . '.' . $item . "\n";
+ }
+ while (1) {
+ print STDOUT $msg . "\n$menu";
+ my $answer = get_input (">");
+
+ # blank and escape answer accepted as undef
+ return undef if $answer =~ /^\s*$/o;
+ return undef
+ if length $answer == 1 && $answer eq "\e";
+
+ # invalid answer not accepted
+ if (length $answer > 1 || ($answer lt 'a' || $answer gt $max_char) ) {
+ print STDOUT "(Please enter a-$max_char)\n";
+ next;
+ }
+
+ # valid answer
+ return $data[ord($answer)-ord('a')];
+ }
+}
+
__END__
From kawas at dev.open-bio.org Thu Nov 16 16:57:42 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 16:57:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162157.kAGLvgjE013105@dev.open-bio.org>
kawas
Thu Nov 16 16:57:41 EST 2006
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv13070/Java/docs
Modified Files:
RegistryServlets.html
Log Message:
added a new way for installing the codebase (ant).
moby-live/Java/docs RegistryServlets.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/RegistryServlets.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2006/10/17 13:42:53 1.3
+++ /home/repository/moby/moby-live/Java/docs/RegistryServlets.html 2006/11/16 21:57:41 1.4
@@ -44,18 +44,43 @@
Installing the Servlets
-Installing the servlets is extremely straight-forward and quite easy.
+Installing the servlets is extremely straight-forward and quite easy. You have 2 choices for installation: use a graphical installer or build your own installation using the latest codebase.
+A. Using the Installer:
- - Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
-
-
- - From the command line, enter the following command
- java -jar install.jar
- A GUI should result that will guide you through the installation process.
-
- - Your done! Now all you have to do is configure your newly installed servlets.
+
+
+ - Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
+
+
+ - From the command line, enter the following command
+ java -jar install.jar
+ A GUI should result that will guide you through the installation process.
+
+ - You're done! Now all you have to do is configure your newly installed servlets.
+
+
+
+B. Building your own installation from the cvs
+
+
+
+ - Please familiarize yourself with the information here for getting and building jMOBY from the cvs.
+
+
+ - From the command line, enter the following command from a *nix box
+ ./build.sh bindist_registry
+ Or the following on a windows machine:
+
+ build.bat bindist_registry
+
+ - Once the build is complete, a zip file will be located at /moby-live/Java/build/registry_servlets called authority.zip. Unzip this file into the webapps directory of Tomcat or other J2EE container.
+
+
+ - You're done. All that is left for you to do is configure the newly installed servlets.
+
+
+
-
Configuring Your Servlets
To Configure the servlets, you must know the following details regarding your local registry:
From kawas at dev.open-bio.org Thu Nov 16 17:00:01 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:00:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162200.kAGM013c013147@dev.open-bio.org>
kawas
Thu Nov 16 17:00:01 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets
In directory dev.open-bio.org:/tmp/cvs-serv13113/Java/src/support/registry-servlets
Log Message:
Directory /home/repository/moby/moby-live/Java/src/support/registry-servlets added to the repository
moby-live/Java/src/support/registry-servlets - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/RCS/directory,v: No such file or directory
From kawas at dev.open-bio.org Thu Nov 16 17:00:06 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:00:06 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162200.kAGM06uW013201@dev.open-bio.org>
kawas
Thu Nov 16 17:00:05 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets
In directory dev.open-bio.org:/tmp/cvs-serv13170/Java/src/support/registry-servlets
Added Files:
moby_ajax.js LSID_resolver.jsp memory.jsp RDFAgent_test.jsp
output.jsp mobyComplete.css top.jsp moby.jsp input.jsp
bottom.jsp stylesheet.css moby_complete.js
Log Message:
some jsp pages, css and js files used by the registry servlets.
moby-live/Java/src/support/registry-servlets moby_ajax.js,NONE,1.1 LSID_resolver.jsp,NONE,1.1 memory.jsp,NONE,1.1 RDFAgent_test.jsp,NONE,1.1 output.jsp,NONE,1.1 mobyComplete.css,NONE,1.1 top.jsp,NONE,1.1 moby.jsp,NONE,1.1 input.jsp,NONE,1.1 bottom.jsp,NONE,1.1 stylesheet.css,NONE,1.1 moby_complete.js,NONE,1.1
From kawas at dev.open-bio.org Thu Nov 16 17:00:28 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:00:28 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162200.kAGM0S8c013240@dev.open-bio.org>
kawas
Thu Nov 16 17:00:28 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets/config
In directory dev.open-bio.org:/tmp/cvs-serv13206/Java/src/support/registry-servlets/config
Log Message:
Directory /home/repository/moby/moby-live/Java/src/support/registry-servlets/config added to the repository
moby-live/Java/src/support/registry-servlets/config - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/config/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/config/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/config/RCS/directory,v: No such file or directory
From kawas at dev.open-bio.org Thu Nov 16 17:00:32 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:00:32 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162200.kAGM0W3N013294@dev.open-bio.org>
kawas
Thu Nov 16 17:00:32 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets/config
In directory dev.open-bio.org:/tmp/cvs-serv13263/Java/src/support/registry-servlets/config
Added Files:
context.xml web.xml server-config.wsdd log4j.properties
default-services.xml
Log Message:
some config files used by the registry servlets
moby-live/Java/src/support/registry-servlets/config context.xml,NONE,1.1 web.xml,NONE,1.1 server-config.wsdd,NONE,1.1 log4j.properties,NONE,1.1 default-services.xml,NONE,1.1
From kawas at dev.open-bio.org Thu Nov 16 17:01:02 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:01:02 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162201.kAGM12Jn013335@dev.open-bio.org>
kawas
Thu Nov 16 17:01:02 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets/data
In directory dev.open-bio.org:/tmp/cvs-serv13301/Java/src/support/registry-servlets/data
Log Message:
Directory /home/repository/moby/moby-live/Java/src/support/registry-servlets/data added to the repository
moby-live/Java/src/support/registry-servlets/data - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/data/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/data/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/support/registry-servlets/data/RCS/directory,v: No such file or directory
From kawas at dev.open-bio.org Thu Nov 16 17:01:05 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:01:05 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162201.kAGM15nw013389@dev.open-bio.org>
kawas
Thu Nov 16 17:01:05 EST 2006
Update of /home/repository/moby/moby-live/Java/src/support/registry-servlets/data
In directory dev.open-bio.org:/tmp/cvs-serv13358/Java/src/support/registry-servlets/data
Added Files:
top.jsp bottom.jsp LSID_resolver.jsp
Log Message:
an lsid client resolver for use by the registry servlets
moby-live/Java/src/support/registry-servlets/data top.jsp,NONE,1.1 bottom.jsp,NONE,1.1 LSID_resolver.jsp,NONE,1.1
From kawas at dev.open-bio.org Thu Nov 16 17:01:50 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:01:50 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162201.kAGM1opH013443@dev.open-bio.org>
kawas
Thu Nov 16 17:01:50 EST 2006
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv13412/Java/xmls
Added Files:
registryServletsBuild.xml
Log Message:
a build file for building the registry servlets.
moby-live/Java/xmls registryServletsBuild.xml,NONE,1.1
From kawas at dev.open-bio.org Thu Nov 16 17:02:14 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Nov 2006 17:02:14 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611162202.kAGM2Een013483@dev.open-bio.org>
kawas
Thu Nov 16 17:02:14 EST 2006
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv13448/Java
Modified Files:
build.xml
Log Message:
updates to the build file to include the registry servlets.
moby-live/Java build.xml,1.59,1.60
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.59
retrieving revision 1.60
diff -u -r1.59 -r1.60
--- /home/repository/moby/moby-live/Java/build.xml 2006/10/25 02:33:22 1.59
+++ /home/repository/moby/moby-live/Java/build.xml 2006/11/16 22:02:14 1.60
@@ -5,6 +5,7 @@
+
@@ -59,6 +60,7 @@
+
@@ -144,6 +146,7 @@
&servletsBuild;
&deployBuild;
&rdfagentBuild;
+ ®istryServletsBuild;
&samplesBuild;
&mosesBuild;
&dashboardBuild;
@@ -165,6 +168,7 @@
+
From mwilkinson at dev.open-bio.org Mon Nov 20 21:41:45 2006
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 20 Nov 2006 21:41:45 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611210241.kAL2fjZp013048@dev.open-bio.org>
mwilkinson
Mon Nov 20 21:41:45 EST 2006
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv13021
Modified Files:
DataClassOntology.html InputMessage.html ObjectStructure.html
Log Message:
fixed some of the documentation, where the links for an invocation message structure were mixed up with the links for a registry call
moby-live/Docs/MOBY-S_API DataClassOntology.html,1.5,1.6 InputMessage.html,1.6,1.7 ObjectStructure.html,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/02/10 17:48:25 1.5
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 02:41:45 1.6
@@ -110,7 +110,7 @@
Notice, these primitive types are the only cases where the content
of the element is meant to be interpreted by the client or service.
-New classes may not inherit from the Primitive Classes. To obtain
+New classes MUST NOT inherit from the Primitive Classes. To obtain
content in another class, you must be a container of a
primitive class. The two relationship types - HASA and HAS - are used
to indicate container relationships, and the contained object is
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/09/22 22:25:55 1.6
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 02:41:45 1.7
@@ -88,10 +88,10 @@
The mobyData
tags delimit the set of inputs to a single
invocation of the service, though there may be multiple
invocations in a single message, each contained within its own
-enumerated mobyData
block. The contents of this block may be a Primary article (mobyData block. The contents of this block may be a Primary
+article (Simple, or Collection),
-or a Secondary article (e.g., a Parameter).
+or a Secondary article, which are Parameters used to modify the service behaviour.
Any request sent to a service with no mobyData
blocks
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/02/10 16:37:09 1.6
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 02:41:45 1.7
@@ -65,7 +65,16 @@
It is our intention that MOBY Objects should be as lightweight as
possible. This not only reduces bandwith, speeds up service response
time, and reduces server load, it also reduces conflict that arises
-from disagreement over the structure of more complex objects.
+from disagreement over the structure of more complex objects. More importantly, however, it results in
+ the creation of Services that have near-transparent semantics. Because of the limited
+ Service Ontology, the functionality of BioMoby services must be clearly
+ described in a single word. Generally speaking, if an Object contains
+ "lots of information", the Service that generates it will be quite complex.
+ Complex services cannot be described in the BioMoby system. As such, BioMoby
+ services attempt to be highly modular - complex data is derived by accessing
+ a broader arrange of lightweight services and integrating this data client-side,
+ in contrast to accessing a "one service provides all" Service whose output consists of many
+ data-types.
MOBY Object structure is inferred by looking up the Object Class in
@@ -133,11 +142,11 @@
The content of the Object element is ignored with the
exception of the Classes representing primitives
-(e.g. Integer, Float, String, etc.; discussed in the Class
-Ontology section below). For example, in the following object
+Ontology). For example, in the following object
- <Object namespace="NCBI_gi" moby:id="163483" > this value is ignored </Object>
+ <moby:Object namespace="NCBI_gi" moby:id="163483" > this value is ignored </Object>
the text "this value is ignored" is ignored by both client and service.
From senger at dev.open-bio.org Tue Nov 21 08:04:15 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 21 Nov 2006 08:04:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211304.kALD4FKt014600@dev.open-bio.org>
senger
Tue Nov 21 08:04:15 EST 2006
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv14563/docs
Modified Files:
ChangeLog
Log Message:
Added "Released-Date" tag to joMby jar files
moby-live/Java/docs ChangeLog,1.74,1.75
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.74
retrieving revision 1.75
diff -u -r1.74 -r1.75
--- /home/repository/moby/moby-live/Java/docs/ChangeLog 2006/10/25 02:33:22 1.74
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2006/11/21 13:04:15 1.75
@@ -1,3 +1,7 @@
+2006-11-21 Martin Senger
+
+ * Added 'Released-Date' tag to joMby jar files
+
2006-10-24 Paul Gordon
* Added Seahawk (MOBY-S client) code to CVS
From senger at dev.open-bio.org Tue Nov 21 08:04:15 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 21 Nov 2006 08:04:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211304.kALD4Fwi014582@dev.open-bio.org>
senger
Tue Nov 21 08:04:15 EST 2006
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv14563
Modified Files:
build.xml
Log Message:
Added "Released-Date" tag to joMby jar files
moby-live/Java build.xml,1.60,1.61
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.60
retrieving revision 1.61
diff -u -r1.60 -r1.61
--- /home/repository/moby/moby-live/Java/build.xml 2006/11/16 22:02:14 1.60
+++ /home/repository/moby/moby-live/Java/build.xml 2006/11/21 13:04:15 1.61
@@ -400,12 +400,15 @@
+
+
+
@@ -413,6 +416,7 @@
+
@@ -421,6 +425,7 @@
includes="org/biomoby/client/ui/** org/biomoby/client/rdf/** org/biomoby/registry/**"/>
+
From senger at dev.open-bio.org Tue Nov 21 08:04:16 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 21 Nov 2006 08:04:16 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211304.kALD4GH7014644@dev.open-bio.org>
senger
Tue Nov 21 08:04:15 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv14563/src/main/org/biomoby/shared
Modified Files:
Central.java
Log Message:
Added "Released-Date" tag to joMby jar files
moby-live/Java/src/main/org/biomoby/shared Central.java,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2005/11/16 08:39:48 1.15
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2006/11/21 13:04:15 1.16
@@ -110,7 +110,7 @@
* values are their authorities
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getServiceNames()
+ Map getServiceNames()
throws MobyException;
/**************************************************************************
@@ -124,7 +124,7 @@
* are arrays of service names provided by each authority
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getServiceNamesByAuthority()
+ Map getServiceNamesByAuthority()
throws MobyException;
/**************************************************************************
@@ -143,7 +143,7 @@
* values are their descriptions
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getServiceTypes()
+ Map getServiceTypes()
throws MobyException;
/**************************************************************************
@@ -171,7 +171,7 @@
* values are their descriptions
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getNamespaces()
+ Map getNamespaces()
throws MobyException;
/**************************************************************************
@@ -191,7 +191,7 @@
* values are their descriptions
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getDataTypeNames()
+ Map getDataTypeNames()
throws MobyException;
/*************************************************************************
@@ -214,7 +214,7 @@
* values (of type String) are data type names.
* @throws MobyException if communication with the Moby Registry fails
*************************************************************************/
- Map getDataTypeRelationships (String dataTypeName)
+ Map getDataTypeRelationships (String dataTypeName)
throws MobyException;
/**************************************************************************
From senger at dev.open-bio.org Tue Nov 21 08:04:15 2006
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 21 Nov 2006 08:04:15 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211304.kALD4FFt014624@dev.open-bio.org>
senger
Tue Nov 21 08:04:15 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv14563/src/main/org/biomoby/client
Modified Files:
CentralImpl.java
Log Message:
Added "Released-Date" tag to joMby jar files
moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.46,1.47
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -r1.46 -r1.47
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2006/09/28 11:54:32 1.46
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2006/11/21 13:04:15 1.47
@@ -161,7 +161,7 @@
}
this.uri = namespace;
- cache = new Hashtable();
+ cache = new Hashtable();
useCache = true;
}
@@ -591,7 +591,7 @@
* that's why I have collect them in an interface.
*
*************************************************************************/
- private Hashtable cache; // this is the cache itself
+ private Hashtable cache; // this is the cache itself
private boolean useCache; // this signal that we are actually caching things
// not used here
@@ -678,13 +678,13 @@
* same name but belonging to different authorities.
*
*************************************************************************/
- public Map getServiceNames()
+ public Map getServiceNames()
throws MobyException {
String result = (String)doCall ("retrieveServiceNames",
new Object[] {});
// parse returned XML
- Map results = new TreeMap (getStringComparator());
+ Map results = new TreeMap (getStringComparator());
Document document = loadDocument (new ByteArrayInputStream (result.getBytes()));
NodeList list = document.getElementsByTagName ("serviceName");
for (int i = 0; i < list.getLength(); i++) {
From kawas at dev.open-bio.org Tue Nov 21 13:46:01 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 21 Nov 2006 13:46:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211846.kALIk1ld015509@dev.open-bio.org>
kawas
Tue Nov 21 13:46:01 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom
In directory dev.open-bio.org:/tmp/cvs-serv15474/Java/src/main/org/biomoby/shared/mobyxml/jdom
Log Message:
Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom added to the repository
moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom - New directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/-,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/New,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/directory,v: No such file or directory
From kawas at dev.open-bio.org Tue Nov 21 13:52:23 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 21 Nov 2006 13:52:23 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211852.kALIqNhe015586@dev.open-bio.org>
kawas
Tue Nov 21 13:52:22 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom
In directory dev.open-bio.org:/tmp/cvs-serv15555/Java/src/main/org/biomoby/shared/mobyxml/jdom
Added Files:
MobyObjectClassNSImpl.java MobyObjectClass.java
MobyObjectClassImpl.java jDomUtilities.java
Log Message:
Some classes that taverna uses. Please do not use these classes as i am weening the taverna plugin off these classes (and I am only committing them because people would like to version jmoby.jar).
moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom MobyObjectClassNSImpl.java,NONE,1.1 MobyObjectClass.java,NONE,1.1 MobyObjectClassImpl.java,NONE,1.1 jDomUtilities.java,NONE,1.1
From gordonp at dev.open-bio.org Tue Nov 21 14:11:24 2006
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 21 Nov 2006 14:11:24 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211911.kALJBOkr015670@dev.open-bio.org>
gordonp
Tue Nov 21 14:11:23 EST 2006
Update of /home/repository/moby/jars-archive/current
In directory dev.open-bio.org:/tmp/cvs-serv15635
Modified Files:
MobyServlet.war
Log Message:
Update to make Taverna-compatible
jars-archive/current MobyServlet.war,1.5,1.6
===================================================================
RCS file: /home/repository/moby/jars-archive/current/MobyServlet.war,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
Binary files /home/repository/moby/jars-archive/current/MobyServlet.war 2006/10/31 20:55:44 1.5 and /home/repository/moby/jars-archive/current/MobyServlet.war 2006/11/21 19:11:23 1.6 differ
rcsdiff: /home/repository/moby/jars-archive/current/MobyServlet.war: diff failed
From mwilkinson at dev.open-bio.org Tue Nov 21 14:15:29 2006
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Tue, 21 Nov 2006 14:15:29 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611211915.kALJFTpj015745@dev.open-bio.org>
mwilkinson
Tue Nov 21 14:15:28 EST 2006
Update of /home/repository/moby/moby-live/Perl/t
In directory dev.open-bio.org:/tmp/cvs-serv15729
Removed Files:
dbConnect.t
Log Message:
no more Perl LSID authority, so no need to test for this module
moby-live/Perl/t dbConnect.t,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Perl/t/RCS/dbConnect.t,v: No such file or directory
From kawas at dev.open-bio.org Tue Nov 21 15:41:35 2006
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 21 Nov 2006 15:41:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611212041.kALKfZdc016077@dev.open-bio.org>
kawas
Tue Nov 21 15:41:35 EST 2006
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom
In directory dev.open-bio.org:/tmp/cvs-serv16042/jdom
Removed Files:
MobyObjectClass.java MobyObjectClassImpl.java
MobyObjectClassNSImpl.java jDomUtilities.java
Log Message:
removing jdom/*
moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom MobyObjectClass.java,1.1,NONE MobyObjectClassImpl.java,1.1,NONE MobyObjectClassNSImpl.java,1.1,NONE jDomUtilities.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/MobyObjectClass.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/MobyObjectClassImpl.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/MobyObjectClassNSImpl.java,v: No such file or directory
rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/mobyxml/jdom/RCS/jDomUtilities.java,v: No such file or directory
From gordonp at dev.open-bio.org Tue Nov 21 16:02:05 2006
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Tue, 21 Nov 2006 16:02:05 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200611212102.kALL25KQ016259@dev.open-bio.org>
gordonp
Tue Nov 21 16:02:05 EST 2006
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv16224/docs
Modified Files:
deployingServices.html
Log Message:
Changed example program to reflect package change for MobyServlet
moby-live/Java/docs deployingServices.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/deployingServices.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/docs/deployingServices.html 2006/10/24 19:11:06 1.9
+++ /home/repository/moby/moby-live/Java/docs/deployingServices.html 2006/11/21 21:02:05 1.10
@@ -71,7 +71,7 @@
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.data.*;
-public class ConvertAAtoFASTA_AA extends org.biomoby.client.MobyServlet{
+public class ConvertAAtoFASTA_AA extends org.biomoby.service.MobyServlet{
public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{
// The input parameter for this method is registered as "inseq"
@@ -340,7 +340,7 @@
Paul Gordon
-Last modified: Wed Aug 2 07:57:12 MDT 2006
+Last modified: Tue Nov 21 13:16:31 MST 2006