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:

    -
  1. Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
    -
    -
  2. -
  3. From the command line, enter the following command
    -
    java -jar install.jar
    -

    A GUI should result that will guide you through the installation process.

    -
  4. -
  5. Your done! Now all you have to do is configure your newly installed servlets.
  6. +
      +
        +
      1. Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
        +
        +
      2. +
      3. From the command line, enter the following command
        +
        java -jar install.jar
        +

        A GUI should result that will guide you through the installation process.

        +
      4. +
      5. You're done! Now all you have to do is configure your newly installed servlets.
      6. +
      +
    +
+

B. Building your own installation from the cvs

+
    +
      +
        +
      1. Please familiarize yourself with the information here for getting and building jMOBY from the cvs.
        +
        +
      2. +
      3. 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
        +
      4. +
      5. 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.
        +
        +
      6. +
      7. You're done. All that is left for you to do is configure the newly installed servlets.
      8. +
      +

      +
-

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 From gordonp at dev.open-bio.org Tue Nov 21 16:02:27 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 21 Nov 2006 16:02:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212102.kALL2RFP016302@dev.open-bio.org> gordonp Tue Nov 21 16:02:26 EST 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv16267/docs Modified Files: tomcatInstall.html Log Message: Fixed list item typo moby-live/Java/docs tomcatInstall.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/tomcatInstall.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/tomcatInstall.html 2006/08/01 15:20:53 1.1 +++ /home/repository/moby/moby-live/Java/docs/tomcatInstall.html 2006/11/21 21:02:26 1.2 @@ -68,7 +68,7 @@
    • Unix/Linux/MacOSX:
      /usr/local/apache-tomcat-5.5.17/bin/startup.sh
    • -
    • Windows: Click your start menu or system tray icon.
    • +
    • Windows: Click your start menu or system tray icon.
    @@ -84,7 +84,7 @@
    Paul Gordon
    -Last modified: Mon Jul 31 13:15:12 MDT 2006 +Last modified: Tue Nov 21 13:17:49 MST 2006 From gordonp at dev.open-bio.org Tue Nov 21 16:03:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 21 Nov 2006 16:03:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212103.kALL3nO5016345@dev.open-bio.org> gordonp Tue Nov 21 16:03:48 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv16310/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: Made code more lenient about receiving MOBY payloads without XML declarations (to accomodate Taverna's bug) moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2006/10/25 02:33:23 1.20 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2006/11/21 21:03:48 1.21 @@ -622,17 +622,28 @@ // by base64 decoding the contents. This is technically not allowable in the // MOBY spec, but we are being lenient. if(!localResponseString.startsWith("\n"+localResponseString; + debugPS.println("Warning: The MOBY contents was missing an XML declaration, but it is " + + "required by the MOBY API, and may stop working in the future without it. Please " + + "contact the client's provider to correct this."); + } + else{ + String oldResponse = localResponseString; + localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString)); + if(!localResponseString.startsWith(" mwilkinson Tue Nov 21 17:49:12 EST 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv16585 Modified Files: Articles.html CentralRegistry.html DataClassOntology.html Examples.html ExceptionCodes.html ExceptionReporting.html InformationBlocks.html InputMessage.html MessageStructure.html MobyCentralObjects.html ObjectStructure.html ObsoleteExceptionMechanism.html OntologyExamples.html OutputMessage.html PrimaryArticle.html RFC.html SecondaryArticle.html XMLPayloads.html index_API.html Log Message: removed incorrect documentation link in all files using perl inplace edit. Hopefully I didnt mess them up... moby-live/Docs/MOBY-S_API Articles.html,1.6,1.7 CentralRegistry.html,1.9,1.10 DataClassOntology.html,1.6,1.7 Examples.html,1.4,1.5 ExceptionCodes.html,1.4,1.5 ExceptionReporting.html,1.6,1.7 InformationBlocks.html,1.5,1.6 InputMessage.html,1.7,1.8 MessageStructure.html,1.9,1.10 MobyCentralObjects.html,1.5,1.6 ObjectStructure.html,1.7,1.8 ObsoleteExceptionMechanism.html,1.3,1.4 OntologyExamples.html,1.5,1.6 OutputMessage.html,1.4,1.5 PrimaryArticle.html,1.4,1.5 RFC.html,1.4,1.5 SecondaryArticle.html,1.7,1.8 XMLPayloads.html,1.15,1.16 index_API.html,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.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/Articles.html 2006/02/10 16:37:09 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 22:49:12 1.7 @@ -184,7 +184,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/02/10 17:48:25 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 22:49:12 1.10 @@ -313,7 +313,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.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/DataClassOntology.html 2006/11/21 02:41:45 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 22:49:12 1.7 @@ -209,7 +209,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/02/10 16:37:09 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/11/21 22:49:12 1.5 @@ -140,7 +140,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/11/21 22:49:12 1.5 @@ -255,7 +255,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.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/ExceptionReporting.html 2006/02/21 15:28:51 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 22:49:12 1.7 @@ -327,7 +327,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.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/InformationBlocks.html 2006/08/24 12:14:20 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2006/11/21 22:49:12 1.6 @@ -260,7 +260,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 02:41:45 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 22:49:12 1.8 @@ -299,7 +299,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/02/21 15:28:51 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 22:49:12 1.10 @@ -221,7 +221,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.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/MobyCentralObjects.html 2006/02/24 16:19:23 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2006/11/21 22:49:12 1.6 @@ -319,7 +319,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 02:41:45 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 22:49:12 1.8 @@ -269,7 +269,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/02/10 16:37:09 1.3 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 22:49:12 1.4 @@ -180,7 +180,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.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/OntologyExamples.html 2006/02/10 16:37:09 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.html 2006/11/21 22:49:12 1.6 @@ -193,7 +193,7 @@
  • RFC
  • -
  • Service API
  • +
  • Categories

    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/11/21 22:49:12 1.5 @@ -245,7 +245,7 @@
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    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/09/07 20:52:15 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/11/21 22:49:12 1.5 @@ -195,7 +195,7 @@
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    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/11/21 22:49:12 1.5 @@ -173,7 +173,7 @@
  • RFC
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    =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/08/15 18:33:25 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 22:49:12 1.11 @@ -220,7 +220,7 @@
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    From mwilkinson at dev.open-bio.org Tue Nov 21 18:04:28 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 21 Nov 2006 18:04:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212304.kALN4SZb016848@dev.open-bio.org> mwilkinson Tue Nov 21 18:04:27 EST 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv16757 Modified Files: Articles.html CentralRegistry.html DataClassOntology.html Examples.html ExceptionCodes.html ExceptionReporting.html InformationBlocks.html InputMessage.html MessageStructure.html MobyCentralObjects.html ObjectStructure.html ObsoleteExceptionMechanism.html OntologyExamples.html OutputMessage.html PrimaryArticle.html RFC.html SecondaryArticle.html XMLPayloads.html index_API.html Log Message: modified documentation hierarchy in right-hand panel to make clearer separation between registry API and service invocation API moby-live/Docs/MOBY-S_API Articles.html,1.7,1.8 CentralRegistry.html,1.10,1.11 DataClassOntology.html,1.7,1.8 Examples.html,1.5,1.6 ExceptionCodes.html,1.5,1.6 ExceptionReporting.html,1.7,1.8 InformationBlocks.html,1.6,1.7 InputMessage.html,1.8,1.9 MessageStructure.html,1.10,1.11 MobyCentralObjects.html,1.6,1.7 ObjectStructure.html,1.8,1.9 ObsoleteExceptionMechanism.html,1.4,1.5 OntologyExamples.html,1.6,1.7 OutputMessage.html,1.5,1.6 PrimaryArticle.html,1.5,1.6 RFC.html,1.5,1.6 SecondaryArticle.html,1.8,1.9 XMLPayloads.html,1.16,1.17 index_API.html,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 23:04:27 1.8 @@ -139,17 +139,18 @@

    Other parts of MOBY-S API

    • API main page
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        +
      • Registry API
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      • DataClassOntology
      • Examples
      • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 22:49:12 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 23:04:27 1.11 @@ -268,17 +268,18 @@

        Other parts of MOBY-S API

        • API main page
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            +
          • Registry API
          • +
          • DataClassOntology
          • Examples
          • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 23:04:27 1.8 @@ -164,17 +164,18 @@

            Other parts of MOBY-S API

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            • Central Registry (MOBY Central) +
                +
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              • Examples
              • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.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/Examples.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/11/21 23:04:27 1.6 @@ -95,17 +95,18 @@

                Other parts of MOBY-S API

                • API main page
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                    +
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                  • Examples
                  • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.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/ExceptionCodes.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/11/21 23:04:27 1.6 @@ -210,17 +210,18 @@

                    Other parts of MOBY-S API

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                        +
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                      • Examples
                      • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 23:04:27 1.8 @@ -282,17 +282,18 @@

                        Other parts of MOBY-S API

                        • API main page
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                            +
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                          • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.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/InformationBlocks.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2006/11/21 23:04:27 1.7 @@ -215,17 +215,18 @@

                            Other parts of MOBY-S API

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                              • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 23:04:27 1.9 @@ -254,17 +254,18 @@

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                                  • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 22:49:12 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 23:04:27 1.11 @@ -176,17 +176,18 @@

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                                      • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.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/MobyCentralObjects.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2006/11/21 23:04:27 1.7 @@ -274,17 +274,18 @@

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                                          • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 23:04:27 1.9 @@ -224,17 +224,18 @@

                                            Other parts of MOBY-S API

                                            • API main page
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                                              • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 22:49:12 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 23:04:27 1.5 @@ -135,17 +135,18 @@

                                                Other parts of MOBY-S API

                                                • API main page
                                                • -
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                                                    +
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                                                  • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.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/OntologyExamples.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.html 2006/11/21 23:04:27 1.7 @@ -148,17 +148,18 @@

                                                    Other parts of MOBY-S API

                                                    • API main page
                                                    • -
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                                                    • Central Registry (MOBY Central) +
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                                                      • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.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/OutputMessage.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/11/21 23:04:27 1.6 @@ -200,17 +200,18 @@

                                                        Other parts of MOBY-S API

                                                        • API main page
                                                        • -
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                                                            +
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                                                          • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.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/PrimaryArticle.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/11/21 23:04:27 1.6 @@ -150,17 +150,18 @@

                                                            Other parts of MOBY-S API

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                                                              • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.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/RFC.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/11/21 23:04:27 1.6 @@ -128,17 +128,18 @@

                                                                Other parts of MOBY-S API

                                                                • API main page
                                                                • -
                                                                • Articles
                                                                • +
                                                                • Central Registry (MOBY Central) +
                                                                    +
                                                                  • Registry API
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                                                                  • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2006/11/21 23:04:27 1.9 @@ -155,17 +155,18 @@

                                                                    Other parts of MOBY-S API

                                                                    • API main page
                                                                    • -
                                                                    • Articles
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                                                                    • Central Registry (MOBY Central) +
                                                                        +
                                                                      • Registry API
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                                                                      • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/11/21 22:49:12 1.16 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/11/21 23:04:27 1.17 @@ -961,17 +961,18 @@

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                                                                          • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 22:49:12 1.11 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 23:04:27 1.12 @@ -175,17 +175,18 @@

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                                                                              • From gordonp at dev.open-bio.org Wed Nov 22 17:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNtxi019938@dev.open-bio.org> gordonp Wed Nov 22 17:23:55 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv19867/xmls Modified Files: seahawkBuild.xml Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/xmls seahawkBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/10/26 01:32:06 1.2 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/22 22:23:55 1.3 @@ -8,51 +8,61 @@ + - + + + + + + + + + + + + + + + + + + + - + + + + - + - + - - --> + - + From gordonp at dev.open-bio.org Wed Nov 22 17:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNtU5019902@dev.open-bio.org> gordonp Wed Nov 22 17:23:54 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-serv19867/src/main/ca/ucalgary/seahawk/gui/test Modified Files: SeahawkTestCase.java Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test SeahawkTestCase.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2006/10/25 13:54:50 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2006/11/22 22:23:54 1.3 @@ -30,11 +30,11 @@ import java.io.File; import java.net.URL; import java.util.List; +import java.util.Vector; public class SeahawkTestCase extends JFCTestCase{ - private final static String TEST_MOBYEX_XML = "testdata/moby_exception.xml"; - //private final static String TEST_MOBY_XML = "testdata/runNCBIBlastn18884.xml"; - private final static String TEST_MOBY_XML = "testdata/allDataTypes.xml"; + private final static String TEST_MOBYEX_XML = "ca/ucalgary/seahawk/gui/test/moby_exception.xml"; + private final static String TEST_MOBY_XML = "ca/ucalgary/seahawk/gui/test/allDataTypes.xml"; private final static String TEST_EXTERNAL_URL = "http://www.google.com/"; private final static String TEST_DNA_SEQ = "AAGCTTGGCCAACGTAAATCTTTCGGCGGCA"; @@ -604,7 +604,7 @@ robot.mouseMove(screenPos.x, screenPos.y); robot.mousePress(InputEvent.BUTTON1_MASK); robot.mouseRelease(InputEvent.BUTTON1_MASK); - sleep(3000); + sleep(2000); finder.setName(MobyContentPane.MOBY_SERVICE_POPUP_NAME); Object openPopup = finder.find(); assertNotNull("Clicking the hyperlink did not open the service options popup (was null)", @@ -641,61 +641,23 @@ serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); } } - assertNotNull("Could not find Parsing services submenu required to test service execution", - serviceTypeChosen); - Point submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - serviceTypeChoices = serviceTypeChosen; - - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(1); - for(int i = 2; - serviceTypeChosen.getText().indexOf("Analysis") == -1 && - i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceTypeChosen = null; break; - } - else{ - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - assertNotNull("Could not find Parsing services submenu required to test service execution", + assertNotNull("Could not find Analysis services submenu required to test service execution", serviceTypeChosen); - submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - serviceTypeChoices = serviceTypeChosen; + Point submenuPos = serviceTypeChosen.getLocationOnScreen(); + // Put mouse on parsing service item to show submenu... + robot.mouseMove(submenuPos.x, submenuPos.y); + sleep(1000); + serviceTypeChoices = serviceTypeChosen; - JMenuItem serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - for(int i = 1; - serviceChosen.getText().indexOf("...") == -1 && i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceChosen = null; break; - } - else{ - serviceChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - if(serviceChosen == null){ + Vector servicePathChosen = findMenuItem((JMenu) serviceTypeChosen, "..."); + if(servicePathChosen == null || servicePathChosen.size() == 0){ System.err.println("WARNING: Skipping test of secondary param services, none were found ending in '...'"); - serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - serviceChosen.doClick(300); - sleep(2000); - DialogFinder dfinder = new DialogFinder(".*"); - List showingDialogs = dfinder.findAll(); - for(int i = 0; i < showingDialogs.size(); i++){ - JDialog dialog = (JDialog) showingDialogs.get(i); - assertFalse("Dialogs with title \""+MobySecondaryInputGUI.TITLE+ - "\" was found, but service launched had no secondary params", - MobySecondaryInputGUI.TITLE.equals(dialog.getTitle())); - } + return; } else{ - Point serviceMenuItemLoc = serviceChosen.getLocationOnScreen(); //so move the mouse there too + // Make sure it's visible + showMenuItem((JMenu) serviceTypeChosen, servicePathChosen, robot); + Point serviceMenuItemLoc = servicePathChosen.lastElement().getLocationOnScreen(); //so move the mouse there too // and click the service button robot.mouseMove(serviceMenuItemLoc.x+2, serviceMenuItemLoc.y+2); robot.keyPress(KeyEvent.VK_SHIFT); @@ -758,7 +720,7 @@ File testFile = File.createTempFile("test-seahawk", ""); testFile.deleteOnExit(); MobySaveDialog.exportSCUFL(contentGUI.getCurrentPane(), testFile); - sleep(2000); + sleep(1000); assertTrue("The SCUFL saved data file was empty", testFile.length() != 0); } @@ -847,46 +809,15 @@ } sleep(500); //give time to draw the menu again - // Pick a service that doesn't take secondary parameters Parsing -> ExplodeOutCrossReferences - assertTrue("There was not at least 2 items (clipboard + a real service) in the service popup submenu", - ((JMenu) serviceTypeChoices).getItemCount() > 1); - JMenuItem serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(1); - for(int i = 2; - serviceTypeChosen.getText().indexOf("Parsing") == -1 && - i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceTypeChosen = null; break; - } - else{ - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - assertNotNull("Could not find Parsing services submenu required to test service execution", - serviceTypeChosen); - Point submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - - JMenuItem serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - for(int i = 1; - serviceChosen.getText().indexOf("ExplodeOutCrossReferences") == -1 && - i <= ((JMenu) serviceTypeChosen).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChosen).getItemCount()){ - serviceChosen = null; break; - } - else{ - serviceChosen = ((JMenu) serviceTypeChosen).getItem(i); - } - } - if(serviceChosen == null){ - System.err.println("Skipping test of non-secondary param services, none were found"); + Vector servicePathChosen = findMenuItem((JMenu) serviceTypeChoices, "ExplodeOutCrossReferences"); + if(servicePathChosen == null || servicePathChosen.size() == 0){ + System.err.println("WARNING: Skipping test of service run, no 'ExplodeOutCrossReferences' service was found"); return; } + // Make sure it's visible + showMenuItem((JMenu) serviceTypeChoices, servicePathChosen, robot); - serviceChosen.doClick(300); + servicePathChosen.lastElement().doClick(300); sleep(2000); DialogFinder dfinder = new DialogFinder(".*"); List showingDialogs = dfinder.findAll(); @@ -945,4 +876,55 @@ junit.textui.TestRunner.run(suite()); } + + public void showMenuItem(JMenu menu, Vector path, Robot robot) throws Exception{ + for(int i = 0; i < path.size(); i++){ + JMenuItem pathItem = path.elementAt(i); + for(int j = 0; j < menu.getItemCount(); j++){ + if(pathItem.equals(menu.getItem(j))){ + Point serviceMenuItemLoc = pathItem.getLocationOnScreen(); //so move the mouse there too + // and click the service button + robot.mouseMove(serviceMenuItemLoc.x+2, serviceMenuItemLoc.y+2); + if(pathItem instanceof JMenu){ //not terminal + menu = (JMenu) pathItem; + } + else{ + i = path.size(); //terminal, end outer loop + } + Thread.sleep(1000); + break; + } + } + } + } + + // Depth-first search of submenus for a menu item matching the pattern + public Vector findMenuItem(JMenu menu, String pattern){ + Vector result = new Vector(); + findMenuItem(menu, pattern, result); + return result; + } + + public boolean findMenuItem(JMenu menu, String pattern, Vector result){ + JMenuItem serviceChosen = menu.getItem(0); + for(int i = 1; + serviceChosen.getText().indexOf(pattern) == -1 && i <= menu.getItemCount(); + i++){ + if(i == menu.getItemCount()){ + return false; + } + else{ + serviceChosen = menu.getItem(i); + // Nested menu + if(serviceChosen instanceof JMenu){ + if(findMenuItem((JMenu) serviceChosen, pattern, result)){ + break; + } + } + } + } + result.insertElementAt(serviceChosen, 0); //build the menu tree path + //System.err.println("Returning menu element " + serviceChosen); + return true; + } } From gordonp at dev.open-bio.org Wed Nov 22 17:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNt7h019920@dev.open-bio.org> gordonp Wed Nov 22 17:23:55 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv19867/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2006/10/25 02:33:23 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2006/11/22 22:23:55 1.2 @@ -40,6 +40,9 @@ public static final String MOBY_INPUT_PARAM = "mobyInput"; public static final String MOBY_SECONDARY_PARAM = "mobySecondaryInput"; public static final String MOBY_OUTPUT_PARAM = "mobyOutput"; + public static final String MODE_HTTP_PARAM = "mode"; + public static final String RDF_MODE = "rdf"; + public static final String ADMIN_MODE = "admin"; public static final int INIT_OUTPUT_BUFFER_SIZE = 100000; protected static MobyRequest mobyRequest; @@ -56,6 +59,8 @@ protected MobyContentInstance currentContent = null; protected boolean isInitialized = false; + /** Changing this value makes logging more or less verbose */ + protected boolean isDebug = false; protected void doGet(HttpServletRequest request, HttpServletResponse response) @@ -68,7 +73,44 @@ } } + // Depending on the argument given, print the RDF signature, + // the admin page, or a Web interface to the program + String mode = request.getParameter(MODE_HTTP_PARAM); + if(mode == null){ // Normal web-browser form fill-in + writeHTMLForm(request, response); + } + else if(mode.equals(RDF_MODE)){ + writeRDF(response); + } + else{ // Unrecognized, print form + writeHTMLForm(request, response); + } + } + + protected void writeHTMLForm(HttpServletRequest request, + HttpServletResponse response){ + java.io.OutputStream out = null; + response.setContentType("text/html"); + try{ + out = response.getOutputStream(); + } + catch(java.io.IOException ioe){ + log("While getting servlet output stream (for HTML form response to client)", ioe); + return; + } + + try{ + out.write("This is where the HTML form would go".getBytes()); + } + catch(java.io.IOException ioe){ + log("While printing HTML form to servlet output stream", ioe); + return; + } + } + + protected void writeRDF(HttpServletResponse response){ java.io.OutputStream out = null; + response.setContentType("text/xml"); try{ out = response.getOutputStream(); } @@ -87,7 +129,13 @@ writer.setProperty("tab", "4"); writer.write(model, stream, null); - out.write(stream.getOutput().getBytes()); + try{ + out.write(stream.getOutput().getBytes()); + } + catch(java.io.IOException ioe){ + log("While printing service RDF to servlet output stream", ioe); + return; + } } protected void doPost(HttpServletRequest request, @@ -474,6 +522,7 @@ else{ mobyRequest = new MobyRequest(new CentralCachedCallsImpl()); } + mobyRequest.setDebugMode(isDebug); }catch(Exception e){ System.err.println("Could not create required resources:"+e); @@ -482,7 +531,7 @@ isInitialized = true; } - private MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{ + private synchronized MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{ MobyService service = new MobyService(getServletName()); Vector inputTypes = new Vector(); @@ -596,7 +645,7 @@ // When we POST this URL, the service is executed service.setURL(endPointURL); // When we GET this URL, the RDF is returned - service.setSignatureURL(endPointURL); + service.setSignatureURL(endPointURL+"?"+MODE_HTTP_PARAM+"="+RDF_MODE); // Other fields (authoritative and contact info) are highly recommended, but optional param = context.getInitParameter(MOBY_AUTHORITATIVE_PARAM); if(param != null){ From gordonp at dev.open-bio.org Wed Nov 22 22:34:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 22:34:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611230334.kAN3Ynwk020296@dev.open-bio.org> gordonp Wed Nov 22 22:34:49 EST 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv20261/docs Modified Files: Seahawk.html Log Message: Fixed markup typo moby-live/Java/docs Seahawk.html,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/Seahawk.html 2006/10/26 01:40:43 1.3 +++ /home/repository/moby/moby-live/Java/docs/Seahawk.html 2006/11/23 03:34:49 1.4 @@ -50,7 +50,7 @@

                                                                                How do I launch it?

                                                                                -

                                                                                The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk/tt>

                                                                                +

                                                                                The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk

                                                                                @@ -121,7 +121,7 @@
                                                                                Paul Gordon
                                                                                -Last modified: Thu Jul 6 14:24:53 MDT 2006 +Last modified: Wed Nov 22 20:32:48 MST 2006 From gordonp at dev.open-bio.org Thu Nov 23 14:28:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Nov 2006 14:28:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611231928.kANJSx2v024829@dev.open-bio.org> gordonp Thu Nov 23 14:28:59 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv24794/src/main/ca/ucalgary/seahawk/util Modified Files: MinJarMaker.java Log Message: Improvements to Minnow completeness (grabbing extra specified files to the JAR from file or other JARs) moby-live/Java/src/main/ca/ucalgary/seahawk/util MinJarMaker.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/11/01 23:45:36 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/11/23 19:28:58 1.3 @@ -5,6 +5,7 @@ import java.util.*; import java.util.jar.*; import java.net.URL; +import java.util.regex.Pattern; /** * This class should be called from the command line using a "clean" JVM @@ -51,7 +52,7 @@ // Check arguments if (args.length < 2) { System.err.println("Usage:\n\n"); - System.err.println("java -cp /dir/containing/only/the/MinJarMaker/class/file -Djarmaker.class.path=$CLASSPATH MinJarMaker main_output.jar [-s | -sw indexoutfile.xml] Program [args...]"); + System.err.println("java -cp /dir/containing/only/the/MinJarMaker/class/file -Djarmaker.class.extras=\"extra/classes/to/include.class\" -Djarmaker.class.path=$CLASSPATH MinJarMaker main_output.jar [-s | -sw indexoutfile.xml] Program [args...]"); System.err.println("Where -s causes the creation of secondary jar files for each package that doesn't"); System.err.println("have all of its classes loaded (i.e. may be loaded in further program execution)"); System.err.println("Where -sw also creates a Web Start document fragment describing the location of"); @@ -439,6 +440,147 @@ jout.closeEntry(); } + protected void addExtraClasses(Set classes){ + StringTokenizer extraClassesTokens = new StringTokenizer(System.getProperty("jarmaker.class.extras"), + File.pathSeparator); + while(extraClassesTokens.hasMoreElements()){ + String classPathElement = extraClassesTokens.nextToken(); + // A literal class to include, not a pattern + if(classPathElement.indexOf("*") == -1){ + byte[] classBytes = null; + try{ + classBytes = getClassBytes(classPathElement); + } + catch(Exception e){ + System.err.println("While trying to get extra class " + classPathElement); + e.printStackTrace(); + } + if(classBytes == null){ + System.err.println("Could not find the specified extra class: " + + classPathElement); + continue; + } + classes.add(classPathElement); + } + // A class pattern that we must find all matches for + else{ + Set matchedClasses = getMatchingClasses(classPathElement); + if(matchedClasses == null || matchedClasses.size() == 0){ + System.err.println("Could not find any classes matching the pattern specified for extra class: " + + classPathElement); + continue; + } + classes.addAll(matchedClasses); + } + } + } + + protected Set findDirMatches(String pathPrefix, File dir, Pattern p, boolean recursive){ + Set matches = new HashSet(); + + String[] files = dir.list(); + for(int i = 0; i < files.length; i++){ + if(files[i].indexOf(".") == 0){ + // skip hidden UNIX files, current dir, parent dir + continue; + } + File file = new File(dir, files[i]); + if(recursive && file.isDirectory()){ + matches.addAll(findDirMatches(pathPrefix, file, p, recursive)); + } + else if(p.matcher(files[i]).matches()){ + // This will mess up on windows, because the file separator \ will be an escape... + matches.add(file.getPath().replace(pathPrefix, "")); + } + } + + return matches; + } + + /** + * The pattern may have the form of an Ant path specification, i.e. "*" matches anything in a directory, + * and "**" matches anything in any subdirectory. + */ + protected Set getMatchingClasses(String pattern){ + Set results = new HashSet(); + + // This code largely copied from the getResourceURL method, with mods for asterisk handling + StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"), + File.pathSeparator); + while(classPathTokens.hasMoreElements()){ + String pathElement = classPathTokens.nextToken(); + String path = pathElement + File.separator + pattern; + String parentPattern = ""; + if(pattern.indexOf(File.separator) != -1 && + pattern.indexOf(File.separator) != pattern.length()-1){ + parentPattern = pattern.substring(0, pattern.lastIndexOf(File.separator)+1); + } + + boolean recursive = false; + if(path.indexOf("**"+File.separator) != -1){ + recursive = true; + path = path.replaceAll("\\*\\*"+File.separator, ""); + parentPattern = parentPattern.replaceAll("\\*\\*"+File.separator, "(.*/)?"); + } + + File pathPattern = new File(path); + File pathParent = pathPattern.getParentFile(); + + // For now, we only take * or ** in the last part of the pattern + // (i.e. specific subdirectories cannot be specified after an asterisk, unless it's in a jar) + String patternWildcard = pathPattern.getName(); + // Turn the asterisked patterns into into regexs + if(patternWildcard.indexOf("**") != -1 && !recursive){ + recursive = true; + } + patternWildcard = patternWildcard.replaceAll("\\.", "\\\\."); // turn all periods into literal periods + patternWildcard = patternWildcard.replaceFirst("\\Q$\\E", "\\\\\\$"); // turn any $ into a literal one + patternWildcard = patternWildcard.replaceAll("\\*{1,2}", ".*"); + // Must match the entirety of the name (anchor start and end of regex + // to start and end of the file name to be compared to) + Pattern filep = Pattern.compile("^"+patternWildcard+"$"); + Pattern jarp = Pattern.compile("^"+parentPattern+ + (recursive ? "(.*/)?" : "") + + patternWildcard.replaceAll(File.separator, "/")+"$"); + + // The path exists in the file system + if(pathParent == null || pathParent.isDirectory()){ + results.addAll(findDirMatches(pathElement + File.separator, pathParent, filep, recursive)); + } + else{ + + // If it's not a valid file system path, 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; + } + + for(Enumeration entries = jarFile.entries(); entries.hasMoreElements();) { + JarEntry entry = entries.nextElement(); + if(jarp.matcher(entry.getName()).matches()){ + results.add(entry.getName()); + } + } + + try{ + jarFile.close(); + } + catch(IOException ioe){ + System.err.println("Couldn't close JAR file: " + pathElement); + } + } //end if file (jar) + } //end else if not dir + } //end for extra class path elements + return results; + } + protected void dumpJar( String jarfile ) throws IOException { // Get the list of classes @@ -447,6 +589,8 @@ corePackages = new Hashtable(); int partId = 1; //ID for part names in JNLP file (shorter than full package name to save space) + addExtraClasses(loadedClasses); + synchronized( loadedClasses ) { // Open up a new JAR file FileOutputStream fout = new FileOutputStream( jarfile ); From gordonp at dev.open-bio.org Thu Nov 23 14:28:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Nov 2006 14:28:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611231928.kANJSxWA024847@dev.open-bio.org> gordonp Thu Nov 23 14:28:59 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24794/xmls Modified Files: seahawkBuild.xml Log Message: Improvements to Minnow completeness (grabbing extra specified files to the JAR from file or other JARs) moby-live/Java/xmls seahawkBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/22 22:23:55 1.3 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/23 19:28:59 1.4 @@ -17,6 +17,7 @@ + @@ -55,10 +56,14 @@ + +
                                                                                + +
                                                                                From gordonp at dev.open-bio.org Fri Nov 24 15:54:17 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:54:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242054.kAOKsHHa028979@dev.open-bio.org> gordonp Fri Nov 24 15:54:16 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test In directory dev.open-bio.org:/tmp/cvs-serv28945/src/main/org/biomoby/service/test Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test added to the repository moby-live/Java/src/main/org/biomoby/service/test - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/directory,v: No such file or directory From gordonp at dev.open-bio.org Fri Nov 24 15:57:25 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:57:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242057.kAOKvPhp029043@dev.open-bio.org> gordonp Fri Nov 24 15:57:25 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv29008/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentPane.java Log Message: Made namespace object retrieval simpler, and changed auth:service format for temp files to avoid invalid file names on Windows (':' isn't allowed in Windows file name apparently) moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.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/gui/MobyContentPane.java 2006/10/25 02:33:22 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2006/11/24 20:57:25 1.2 @@ -452,13 +452,17 @@ } private String serviceToFilePrefix(MobyService service){ - return service.getAuthority()+":"+service.getName()+":"; + return service.getAuthority()+"_SEAHAWk_"+service.getName()+"_SEAHAWk_"; } private MobyService filePrefixToService(String filename) throws Exception{ - StringTokenizer st = new StringTokenizer(filename, ":"); - String auth = st.nextToken(); - String name = st.nextToken(); + String tokens[] = filename.split("_SEAHAWk_"); + if(tokens == null || tokens.length < 2){ + return null; + } + + String auth = tokens[0]; + String name = tokens[1]; if(name == null){ return null; @@ -734,14 +738,7 @@ else{ mobyData = new MobyDataObject(""); } - MobyNamespace ns = new MobyNamespace(namespace); - try{ - ns.setDescription((String) servicesGUI.getMobyCentralImpl().getNamespaces().get(namespace)); - } - catch(MobyException mobye){ - logger.debug("Warning: can't retrieve namespace descriptions: " + mobye); - } - mobyData.addNamespace(ns); + mobyData.addNamespace(MobyNamespace.getNamespace(namespace)); if(mobyID != null){ mobyData.setId(mobyID); From gordonp at dev.open-bio.org Fri Nov 24 15:58:45 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:58:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242058.kAOKwjPj029103@dev.open-bio.org> gordonp Fri Nov 24 15:58:45 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv29072/src/main/ca/ucalgary/seahawk/util Added Files: SplashWindow.java Log Message: Added spalsh screen to application/applet jar of Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/util SplashWindow.java,NONE,1.1 From gordonp at dev.open-bio.org Fri Nov 24 15:58:45 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:58:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242058.kAOKwjrL029123@dev.open-bio.org> gordonp Fri Nov 24 15:58:45 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv29072/src/main/ca/ucalgary/seahawk/gui Modified Files: SeahawkSplasher.java Log Message: Added spalsh screen to application/applet jar of Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/gui SeahawkSplasher.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkSplasher.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/gui/SeahawkSplasher.java 2006/10/25 02:33:22 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkSplasher.java 2006/11/24 20:58:45 1.2 @@ -11,6 +11,7 @@ */ import javax.swing.JApplet; +import ca.ucalgary.seahawk.util.SplashWindow; /** * Modified to support both applet and application modes. From gordonp at dev.open-bio.org Fri Nov 24 16:10:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 16:10:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242110.kAOLAdlU029206@dev.open-bio.org> gordonp Fri Nov 24 16:10:39 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv29171/xmls Modified Files: seahawkBuild.xml Log Message: Added ability to automatically deploy a signed applet (if you have a signing certificate, of course) moby-live/Java/xmls seahawkBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/23 19:28:59 1.4 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/24 21:10:39 1.5 @@ -2,16 +2,23 @@ + + + + - + + + + @@ -49,13 +56,16 @@ - + + + @@ -74,3 +84,56 @@ + + + + + + + + + + + + + + + +
                                                                                + + + +
                                                                                +
                                                                                +
                                                                                + + + + + + + + + +
                                                                                + + + + From gordonp at dev.open-bio.org Mon Nov 27 10:40:33 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 27 Nov 2006 10:40:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611271540.kARFeXfb027537@dev.open-bio.org> gordonp Mon Nov 27 10:40:32 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv27502/src/main/ca/ucalgary/seahawk/util Modified Files: SplashWindow.java Log Message: Fixed javadoc error moby-live/Java/src/main/ca/ucalgary/seahawk/util SplashWindow.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/SplashWindow.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/SplashWindow.java 2006/11/24 20:58:45 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/SplashWindow.java 2006/11/27 15:40:32 1.2 @@ -412,7 +412,7 @@ /** * Invokes the init method of the JApplet class provided by name. - * @param args the applet that was actually launched + * @param applet the applet that was actually launched */ public static void invokeInit(String className, javax.swing.JApplet applet) { From gordonp at dev.open-bio.org Wed Nov 1 23:44:34 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 23:45:36 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 23:46:59 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 23:04:34 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 23:04:34 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 23:04:34 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 21:57:42 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:

                                                                                  -
                                                                                1. Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
                                                                                  -
                                                                                  -
                                                                                2. -
                                                                                3. From the command line, enter the following command
                                                                                  -
                                                                                  java -jar install.jar
                                                                                  -

                                                                                  A GUI should result that will guide you through the installation process.

                                                                                  -
                                                                                4. -
                                                                                5. Your done! Now all you have to do is configure your newly installed servlets.
                                                                                6. +
                                                                                    +
                                                                                      +
                                                                                    1. Download the installation file from http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar
                                                                                      +
                                                                                      +
                                                                                    2. +
                                                                                    3. From the command line, enter the following command
                                                                                      +
                                                                                      java -jar install.jar
                                                                                      +

                                                                                      A GUI should result that will guide you through the installation process.

                                                                                      +
                                                                                    4. +
                                                                                    5. You're done! Now all you have to do is configure your newly installed servlets.
                                                                                    6. +
                                                                                    +
                                                                                  +
                                                                                +

                                                                                B. Building your own installation from the cvs

                                                                                +
                                                                                  +
                                                                                    +
                                                                                      +
                                                                                    1. Please familiarize yourself with the information here for getting and building jMOBY from the cvs.
                                                                                      +
                                                                                      +
                                                                                    2. +
                                                                                    3. 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
                                                                                      +
                                                                                    4. +
                                                                                    5. 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.
                                                                                      +
                                                                                      +
                                                                                    6. +
                                                                                    7. You're done. All that is left for you to do is configure the newly installed servlets.
                                                                                    8. +
                                                                                    +

                                                                                    +
                                                                                -

                                                                                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 22:00:01 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 22:00:06 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 22:00:28 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 22:00:32 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 22:01:02 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 22:01:05 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 22:01:50 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 22:02:14 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 Tue Nov 21 02:41:45 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 13:04:15 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 13:04:15 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 13:04:16 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 13:04:15 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 18:46:01 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 18:52:23 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 19:11:24 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 19:15:29 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 20:41:35 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 21:02:05 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 From gordonp at dev.open-bio.org Tue Nov 21 21:02:27 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 21 Nov 2006 16:02:27 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212102.kALL2RFP016302@dev.open-bio.org> gordonp Tue Nov 21 16:02:26 EST 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv16267/docs Modified Files: tomcatInstall.html Log Message: Fixed list item typo moby-live/Java/docs tomcatInstall.html,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/tomcatInstall.html,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/docs/tomcatInstall.html 2006/08/01 15:20:53 1.1 +++ /home/repository/moby/moby-live/Java/docs/tomcatInstall.html 2006/11/21 21:02:26 1.2 @@ -68,7 +68,7 @@
                                                                                  • Unix/Linux/MacOSX:
                                                                                    /usr/local/apache-tomcat-5.5.17/bin/startup.sh
                                                                                  • -
                                                                                  • Windows: Click your start menu or system tray icon.
                                                                                  • +
                                                                                  • Windows: Click your start menu or system tray icon.
                                                                                  @@ -84,7 +84,7 @@
                                                                                  Paul Gordon
                                                                                  -Last modified: Mon Jul 31 13:15:12 MDT 2006 +Last modified: Tue Nov 21 13:17:49 MST 2006 From gordonp at dev.open-bio.org Tue Nov 21 21:03:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Tue, 21 Nov 2006 16:03:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212103.kALL3nO5016345@dev.open-bio.org> gordonp Tue Nov 21 16:03:48 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory dev.open-bio.org:/tmp/cvs-serv16310/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: Made code more lenient about receiving MOBY payloads without XML declarations (to accomodate Taverna's bug) moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.20,1.21 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2006/10/25 02:33:23 1.20 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2006/11/21 21:03:48 1.21 @@ -622,17 +622,28 @@ // by base64 decoding the contents. This is technically not allowable in the // MOBY spec, but we are being lenient. if(!localResponseString.startsWith("\n"+localResponseString; + debugPS.println("Warning: The MOBY contents was missing an XML declaration, but it is " + + "required by the MOBY API, and may stop working in the future without it. Please " + + "contact the client's provider to correct this."); + } + else{ + String oldResponse = localResponseString; + localResponseString = new String(org.apache.axis.encoding.Base64.decode(localResponseString)); + if(!localResponseString.startsWith(" mwilkinson Tue Nov 21 17:49:12 EST 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv16585 Modified Files: Articles.html CentralRegistry.html DataClassOntology.html Examples.html ExceptionCodes.html ExceptionReporting.html InformationBlocks.html InputMessage.html MessageStructure.html MobyCentralObjects.html ObjectStructure.html ObsoleteExceptionMechanism.html OntologyExamples.html OutputMessage.html PrimaryArticle.html RFC.html SecondaryArticle.html XMLPayloads.html index_API.html Log Message: removed incorrect documentation link in all files using perl inplace edit. Hopefully I didnt mess them up... moby-live/Docs/MOBY-S_API Articles.html,1.6,1.7 CentralRegistry.html,1.9,1.10 DataClassOntology.html,1.6,1.7 Examples.html,1.4,1.5 ExceptionCodes.html,1.4,1.5 ExceptionReporting.html,1.6,1.7 InformationBlocks.html,1.5,1.6 InputMessage.html,1.7,1.8 MessageStructure.html,1.9,1.10 MobyCentralObjects.html,1.5,1.6 ObjectStructure.html,1.7,1.8 ObsoleteExceptionMechanism.html,1.3,1.4 OntologyExamples.html,1.5,1.6 OutputMessage.html,1.4,1.5 PrimaryArticle.html,1.4,1.5 RFC.html,1.4,1.5 SecondaryArticle.html,1.7,1.8 XMLPayloads.html,1.15,1.16 index_API.html,1.10,1.11 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.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/Articles.html 2006/02/10 16:37:09 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 22:49:12 1.7 @@ -184,7 +184,7 @@
                                                                              • RFC
                                                                              • -
                                                                              • Service API
                                                                              • +
                                                                            • Categories

                                                                              =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/02/10 17:48:25 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 22:49:12 1.10 @@ -313,7 +313,7 @@
                                                                          • RFC
                                                                          • -
                                                                          • Service API
                                                                          • +
                                                                        • Categories

                                                                          =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.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/DataClassOntology.html 2006/11/21 02:41:45 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 22:49:12 1.7 @@ -209,7 +209,7 @@
                                                                      • RFC
                                                                      • -
                                                                      • Service API
                                                                      • +
                                                                    • Categories

                                                                      =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/02/10 16:37:09 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/11/21 22:49:12 1.5 @@ -140,7 +140,7 @@
                                                                  • RFC
                                                                  • -
                                                                  • Service API
                                                                  • +
                                                                • Categories

                                                                  =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/11/21 22:49:12 1.5 @@ -255,7 +255,7 @@
                                                              • RFC
                                                              • -
                                                              • Service API
                                                              • +
                                                            • Categories

                                                              =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.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/ExceptionReporting.html 2006/02/21 15:28:51 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 22:49:12 1.7 @@ -327,7 +327,7 @@
                                                          • RFC
                                                          • -
                                                          • Service API
                                                          • +
                                                        • Categories

                                                          =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.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/InformationBlocks.html 2006/08/24 12:14:20 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2006/11/21 22:49:12 1.6 @@ -260,7 +260,7 @@
                                                      • RFC
                                                      • -
                                                      • Service API
                                                      • +
                                                    • Categories

                                                      =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 02:41:45 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 22:49:12 1.8 @@ -299,7 +299,7 @@
                                                  • RFC
                                                  • -
                                                  • Service API
                                                  • +
                                                • Categories

                                                  =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/02/21 15:28:51 1.9 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 22:49:12 1.10 @@ -221,7 +221,7 @@
                                              • RFC
                                              • -
                                              • Service API
                                              • +
                                            • Categories

                                              =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.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/MobyCentralObjects.html 2006/02/24 16:19:23 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2006/11/21 22:49:12 1.6 @@ -319,7 +319,7 @@
                                          • RFC
                                          • -
                                          • Service API
                                          • +
                                        • Categories

                                          =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 02:41:45 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 22:49:12 1.8 @@ -269,7 +269,7 @@
                                      • RFC
                                      • -
                                      • Service API
                                      • +
                                    • Categories

                                      =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/02/10 16:37:09 1.3 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 22:49:12 1.4 @@ -180,7 +180,7 @@
                                  • RFC
                                  • -
                                  • Service API
                                  • +
                                • Categories

                                  =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.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/OntologyExamples.html 2006/02/10 16:37:09 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.html 2006/11/21 22:49:12 1.6 @@ -193,7 +193,7 @@
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                              =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/11/21 22:49:12 1.5 @@ -245,7 +245,7 @@
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                          =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/09/07 20:52:15 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/11/21 22:49:12 1.5 @@ -195,7 +195,7 @@
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                      =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/02/21 15:28:51 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/11/21 22:49:12 1.5 @@ -173,7 +173,7 @@
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              =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/09/07 20:52:15 1.15 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/11/21 22:49:12 1.16 @@ -1006,7 +1006,7 @@
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          =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/08/15 18:33:25 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 22:49:12 1.11 @@ -220,7 +220,7 @@
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      From mwilkinson at dev.open-bio.org Tue Nov 21 23:04:28 2006 From: mwilkinson at dev.open-bio.org (Mark Wilkinson) Date: Tue, 21 Nov 2006 18:04:28 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611212304.kALN4SZb016848@dev.open-bio.org> mwilkinson Tue Nov 21 18:04:27 EST 2006 Update of /home/repository/moby/moby-live/Docs/MOBY-S_API In directory dev.open-bio.org:/tmp/cvs-serv16757 Modified Files: Articles.html CentralRegistry.html DataClassOntology.html Examples.html ExceptionCodes.html ExceptionReporting.html InformationBlocks.html InputMessage.html MessageStructure.html MobyCentralObjects.html ObjectStructure.html ObsoleteExceptionMechanism.html OntologyExamples.html OutputMessage.html PrimaryArticle.html RFC.html SecondaryArticle.html XMLPayloads.html index_API.html Log Message: modified documentation hierarchy in right-hand panel to make clearer separation between registry API and service invocation API moby-live/Docs/MOBY-S_API Articles.html,1.7,1.8 CentralRegistry.html,1.10,1.11 DataClassOntology.html,1.7,1.8 Examples.html,1.5,1.6 ExceptionCodes.html,1.5,1.6 ExceptionReporting.html,1.7,1.8 InformationBlocks.html,1.6,1.7 InputMessage.html,1.8,1.9 MessageStructure.html,1.10,1.11 MobyCentralObjects.html,1.6,1.7 ObjectStructure.html,1.8,1.9 ObsoleteExceptionMechanism.html,1.4,1.5 OntologyExamples.html,1.6,1.7 OutputMessage.html,1.5,1.6 PrimaryArticle.html,1.5,1.6 RFC.html,1.5,1.6 SecondaryArticle.html,1.8,1.9 XMLPayloads.html,1.16,1.17 index_API.html,1.11,1.12 =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Articles.html 2006/11/21 23:04:27 1.8 @@ -139,17 +139,18 @@

      Other parts of MOBY-S API

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        • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 22:49:12 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/CentralRegistry.html 2006/11/21 23:04:27 1.11 @@ -268,17 +268,18 @@

          Other parts of MOBY-S API

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              +
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            • Examples
            • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/DataClassOntology.html 2006/11/21 23:04:27 1.8 @@ -164,17 +164,18 @@

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                • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.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/Examples.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Examples.html 2006/11/21 23:04:27 1.6 @@ -95,17 +95,18 @@

                  Other parts of MOBY-S API

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                    • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.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/ExceptionCodes.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionCodes.html 2006/11/21 23:04:27 1.6 @@ -210,17 +210,18 @@

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                        • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 22:49:12 1.7 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ExceptionReporting.html 2006/11/21 23:04:27 1.8 @@ -282,17 +282,18 @@

                          Other parts of MOBY-S API

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                            • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.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/InformationBlocks.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InformationBlocks.html 2006/11/21 23:04:27 1.7 @@ -215,17 +215,18 @@

                              Other parts of MOBY-S API

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                                • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InputMessage.html 2006/11/21 23:04:27 1.9 @@ -254,17 +254,18 @@

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                                    • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 22:49:12 1.10 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MessageStructure.html 2006/11/21 23:04:27 1.11 @@ -176,17 +176,18 @@

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                                        • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.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/MobyCentralObjects.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/MobyCentralObjects.html 2006/11/21 23:04:27 1.7 @@ -274,17 +274,18 @@

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                                            • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObjectStructure.html 2006/11/21 23:04:27 1.9 @@ -224,17 +224,18 @@

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                                                • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 22:49:12 1.4 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/ObsoleteExceptionMechanism.html 2006/11/21 23:04:27 1.5 @@ -135,17 +135,18 @@

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                                                    • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.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/OntologyExamples.html 2006/11/21 22:49:12 1.6 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OntologyExamples.html 2006/11/21 23:04:27 1.7 @@ -148,17 +148,18 @@

                                                      Other parts of MOBY-S API

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                                                        • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.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/OutputMessage.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/OutputMessage.html 2006/11/21 23:04:27 1.6 @@ -200,17 +200,18 @@

                                                          Other parts of MOBY-S API

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                                                            • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.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/PrimaryArticle.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/PrimaryArticle.html 2006/11/21 23:04:27 1.6 @@ -150,17 +150,18 @@

                                                              Other parts of MOBY-S API

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                                                                • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.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/RFC.html 2006/11/21 22:49:12 1.5 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/RFC.html 2006/11/21 23:04:27 1.6 @@ -128,17 +128,18 @@

                                                                  Other parts of MOBY-S API

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                                                                    • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html,v retrieving revision 1.8 retrieving revision 1.9 diff -u -r1.8 -r1.9 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2006/11/21 22:49:12 1.8 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/SecondaryArticle.html 2006/11/21 23:04:27 1.9 @@ -155,17 +155,18 @@

                                                                      Other parts of MOBY-S API

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                                                                        • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/11/21 22:49:12 1.16 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2006/11/21 23:04:27 1.17 @@ -961,17 +961,18 @@

                                                                          Other parts of MOBY-S API

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                                                                            • =================================================================== RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 22:49:12 1.11 +++ /home/repository/moby/moby-live/Docs/MOBY-S_API/index_API.html 2006/11/21 23:04:27 1.12 @@ -175,17 +175,18 @@

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                                                                                • From gordonp at dev.open-bio.org Wed Nov 22 22:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNtxi019938@dev.open-bio.org> gordonp Wed Nov 22 17:23:55 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv19867/xmls Modified Files: seahawkBuild.xml Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/xmls seahawkBuild.xml,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/10/26 01:32:06 1.2 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/22 22:23:55 1.3 @@ -8,51 +8,61 @@ + - + + + + + + + + + + + + + + + + + + + - + + + + - + - + - - --> + - + From gordonp at dev.open-bio.org Wed Nov 22 22:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNtU5019902@dev.open-bio.org> gordonp Wed Nov 22 17:23:54 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-serv19867/src/main/ca/ucalgary/seahawk/gui/test Modified Files: SeahawkTestCase.java Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test SeahawkTestCase.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2006/10/25 13:54:50 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/test/SeahawkTestCase.java 2006/11/22 22:23:54 1.3 @@ -30,11 +30,11 @@ import java.io.File; import java.net.URL; import java.util.List; +import java.util.Vector; public class SeahawkTestCase extends JFCTestCase{ - private final static String TEST_MOBYEX_XML = "testdata/moby_exception.xml"; - //private final static String TEST_MOBY_XML = "testdata/runNCBIBlastn18884.xml"; - private final static String TEST_MOBY_XML = "testdata/allDataTypes.xml"; + private final static String TEST_MOBYEX_XML = "ca/ucalgary/seahawk/gui/test/moby_exception.xml"; + private final static String TEST_MOBY_XML = "ca/ucalgary/seahawk/gui/test/allDataTypes.xml"; private final static String TEST_EXTERNAL_URL = "http://www.google.com/"; private final static String TEST_DNA_SEQ = "AAGCTTGGCCAACGTAAATCTTTCGGCGGCA"; @@ -604,7 +604,7 @@ robot.mouseMove(screenPos.x, screenPos.y); robot.mousePress(InputEvent.BUTTON1_MASK); robot.mouseRelease(InputEvent.BUTTON1_MASK); - sleep(3000); + sleep(2000); finder.setName(MobyContentPane.MOBY_SERVICE_POPUP_NAME); Object openPopup = finder.find(); assertNotNull("Clicking the hyperlink did not open the service options popup (was null)", @@ -641,61 +641,23 @@ serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); } } - assertNotNull("Could not find Parsing services submenu required to test service execution", - serviceTypeChosen); - Point submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - serviceTypeChoices = serviceTypeChosen; - - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(1); - for(int i = 2; - serviceTypeChosen.getText().indexOf("Analysis") == -1 && - i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceTypeChosen = null; break; - } - else{ - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - assertNotNull("Could not find Parsing services submenu required to test service execution", + assertNotNull("Could not find Analysis services submenu required to test service execution", serviceTypeChosen); - submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - serviceTypeChoices = serviceTypeChosen; + Point submenuPos = serviceTypeChosen.getLocationOnScreen(); + // Put mouse on parsing service item to show submenu... + robot.mouseMove(submenuPos.x, submenuPos.y); + sleep(1000); + serviceTypeChoices = serviceTypeChosen; - JMenuItem serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - for(int i = 1; - serviceChosen.getText().indexOf("...") == -1 && i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceChosen = null; break; - } - else{ - serviceChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - if(serviceChosen == null){ + Vector servicePathChosen = findMenuItem((JMenu) serviceTypeChosen, "..."); + if(servicePathChosen == null || servicePathChosen.size() == 0){ System.err.println("WARNING: Skipping test of secondary param services, none were found ending in '...'"); - serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - serviceChosen.doClick(300); - sleep(2000); - DialogFinder dfinder = new DialogFinder(".*"); - List showingDialogs = dfinder.findAll(); - for(int i = 0; i < showingDialogs.size(); i++){ - JDialog dialog = (JDialog) showingDialogs.get(i); - assertFalse("Dialogs with title \""+MobySecondaryInputGUI.TITLE+ - "\" was found, but service launched had no secondary params", - MobySecondaryInputGUI.TITLE.equals(dialog.getTitle())); - } + return; } else{ - Point serviceMenuItemLoc = serviceChosen.getLocationOnScreen(); //so move the mouse there too + // Make sure it's visible + showMenuItem((JMenu) serviceTypeChosen, servicePathChosen, robot); + Point serviceMenuItemLoc = servicePathChosen.lastElement().getLocationOnScreen(); //so move the mouse there too // and click the service button robot.mouseMove(serviceMenuItemLoc.x+2, serviceMenuItemLoc.y+2); robot.keyPress(KeyEvent.VK_SHIFT); @@ -758,7 +720,7 @@ File testFile = File.createTempFile("test-seahawk", ""); testFile.deleteOnExit(); MobySaveDialog.exportSCUFL(contentGUI.getCurrentPane(), testFile); - sleep(2000); + sleep(1000); assertTrue("The SCUFL saved data file was empty", testFile.length() != 0); } @@ -847,46 +809,15 @@ } sleep(500); //give time to draw the menu again - // Pick a service that doesn't take secondary parameters Parsing -> ExplodeOutCrossReferences - assertTrue("There was not at least 2 items (clipboard + a real service) in the service popup submenu", - ((JMenu) serviceTypeChoices).getItemCount() > 1); - JMenuItem serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(1); - for(int i = 2; - serviceTypeChosen.getText().indexOf("Parsing") == -1 && - i <= ((JMenu) serviceTypeChoices).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChoices).getItemCount()){ - serviceTypeChosen = null; break; - } - else{ - serviceTypeChosen = ((JMenu) serviceTypeChoices).getItem(i); - } - } - assertNotNull("Could not find Parsing services submenu required to test service execution", - serviceTypeChosen); - Point submenuPos = serviceTypeChosen.getLocationOnScreen(); - // Put mouse on parsing service item to show submenu... - robot.mouseMove(submenuPos.x, submenuPos.y); - sleep(1000); - - JMenuItem serviceChosen = ((JMenu) serviceTypeChosen).getItem(0); - for(int i = 1; - serviceChosen.getText().indexOf("ExplodeOutCrossReferences") == -1 && - i <= ((JMenu) serviceTypeChosen).getItemCount(); - i++){ - if(i == ((JMenu) serviceTypeChosen).getItemCount()){ - serviceChosen = null; break; - } - else{ - serviceChosen = ((JMenu) serviceTypeChosen).getItem(i); - } - } - if(serviceChosen == null){ - System.err.println("Skipping test of non-secondary param services, none were found"); + Vector servicePathChosen = findMenuItem((JMenu) serviceTypeChoices, "ExplodeOutCrossReferences"); + if(servicePathChosen == null || servicePathChosen.size() == 0){ + System.err.println("WARNING: Skipping test of service run, no 'ExplodeOutCrossReferences' service was found"); return; } + // Make sure it's visible + showMenuItem((JMenu) serviceTypeChoices, servicePathChosen, robot); - serviceChosen.doClick(300); + servicePathChosen.lastElement().doClick(300); sleep(2000); DialogFinder dfinder = new DialogFinder(".*"); List showingDialogs = dfinder.findAll(); @@ -945,4 +876,55 @@ junit.textui.TestRunner.run(suite()); } + + public void showMenuItem(JMenu menu, Vector path, Robot robot) throws Exception{ + for(int i = 0; i < path.size(); i++){ + JMenuItem pathItem = path.elementAt(i); + for(int j = 0; j < menu.getItemCount(); j++){ + if(pathItem.equals(menu.getItem(j))){ + Point serviceMenuItemLoc = pathItem.getLocationOnScreen(); //so move the mouse there too + // and click the service button + robot.mouseMove(serviceMenuItemLoc.x+2, serviceMenuItemLoc.y+2); + if(pathItem instanceof JMenu){ //not terminal + menu = (JMenu) pathItem; + } + else{ + i = path.size(); //terminal, end outer loop + } + Thread.sleep(1000); + break; + } + } + } + } + + // Depth-first search of submenus for a menu item matching the pattern + public Vector findMenuItem(JMenu menu, String pattern){ + Vector result = new Vector(); + findMenuItem(menu, pattern, result); + return result; + } + + public boolean findMenuItem(JMenu menu, String pattern, Vector result){ + JMenuItem serviceChosen = menu.getItem(0); + for(int i = 1; + serviceChosen.getText().indexOf(pattern) == -1 && i <= menu.getItemCount(); + i++){ + if(i == menu.getItemCount()){ + return false; + } + else{ + serviceChosen = menu.getItem(i); + // Nested menu + if(serviceChosen instanceof JMenu){ + if(findMenuItem((JMenu) serviceChosen, pattern, result)){ + break; + } + } + } + } + result.insertElementAt(serviceChosen, 0); //build the menu tree path + //System.err.println("Returning menu element " + serviceChosen); + return true; + } } From gordonp at dev.open-bio.org Wed Nov 22 22:23:55 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 17:23:55 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611222223.kAMMNt7h019920@dev.open-bio.org> gordonp Wed Nov 22 17:23:55 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service In directory dev.open-bio.org:/tmp/cvs-serv19867/src/main/org/biomoby/service Modified Files: MobyServlet.java Log Message: Changes to improve Seahawk Unit Test generality moby-live/Java/src/main/org/biomoby/service MobyServlet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2006/10/25 02:33:23 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/MobyServlet.java 2006/11/22 22:23:55 1.2 @@ -40,6 +40,9 @@ public static final String MOBY_INPUT_PARAM = "mobyInput"; public static final String MOBY_SECONDARY_PARAM = "mobySecondaryInput"; public static final String MOBY_OUTPUT_PARAM = "mobyOutput"; + public static final String MODE_HTTP_PARAM = "mode"; + public static final String RDF_MODE = "rdf"; + public static final String ADMIN_MODE = "admin"; public static final int INIT_OUTPUT_BUFFER_SIZE = 100000; protected static MobyRequest mobyRequest; @@ -56,6 +59,8 @@ protected MobyContentInstance currentContent = null; protected boolean isInitialized = false; + /** Changing this value makes logging more or less verbose */ + protected boolean isDebug = false; protected void doGet(HttpServletRequest request, HttpServletResponse response) @@ -68,7 +73,44 @@ } } + // Depending on the argument given, print the RDF signature, + // the admin page, or a Web interface to the program + String mode = request.getParameter(MODE_HTTP_PARAM); + if(mode == null){ // Normal web-browser form fill-in + writeHTMLForm(request, response); + } + else if(mode.equals(RDF_MODE)){ + writeRDF(response); + } + else{ // Unrecognized, print form + writeHTMLForm(request, response); + } + } + + protected void writeHTMLForm(HttpServletRequest request, + HttpServletResponse response){ + java.io.OutputStream out = null; + response.setContentType("text/html"); + try{ + out = response.getOutputStream(); + } + catch(java.io.IOException ioe){ + log("While getting servlet output stream (for HTML form response to client)", ioe); + return; + } + + try{ + out.write("This is where the HTML form would go".getBytes()); + } + catch(java.io.IOException ioe){ + log("While printing HTML form to servlet output stream", ioe); + return; + } + } + + protected void writeRDF(HttpServletResponse response){ java.io.OutputStream out = null; + response.setContentType("text/xml"); try{ out = response.getOutputStream(); } @@ -87,7 +129,13 @@ writer.setProperty("tab", "4"); writer.write(model, stream, null); - out.write(stream.getOutput().getBytes()); + try{ + out.write(stream.getOutput().getBytes()); + } + catch(java.io.IOException ioe){ + log("While printing service RDF to servlet output stream", ioe); + return; + } } protected void doPost(HttpServletRequest request, @@ -474,6 +522,7 @@ else{ mobyRequest = new MobyRequest(new CentralCachedCallsImpl()); } + mobyRequest.setDebugMode(isDebug); }catch(Exception e){ System.err.println("Could not create required resources:"+e); @@ -482,7 +531,7 @@ isInitialized = true; } - private MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{ + private synchronized MobyService createServiceFromConfig(HttpServletRequest request) throws Exception{ MobyService service = new MobyService(getServletName()); Vector inputTypes = new Vector(); @@ -596,7 +645,7 @@ // When we POST this URL, the service is executed service.setURL(endPointURL); // When we GET this URL, the RDF is returned - service.setSignatureURL(endPointURL); + service.setSignatureURL(endPointURL+"?"+MODE_HTTP_PARAM+"="+RDF_MODE); // Other fields (authoritative and contact info) are highly recommended, but optional param = context.getInitParameter(MOBY_AUTHORITATIVE_PARAM); if(param != null){ From gordonp at dev.open-bio.org Thu Nov 23 03:34:49 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Wed, 22 Nov 2006 22:34:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611230334.kAN3Ynwk020296@dev.open-bio.org> gordonp Wed Nov 22 22:34:49 EST 2006 Update of /home/repository/moby/moby-live/Java/docs In directory dev.open-bio.org:/tmp/cvs-serv20261/docs Modified Files: Seahawk.html Log Message: Fixed markup typo moby-live/Java/docs Seahawk.html,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/Seahawk.html,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/docs/Seahawk.html 2006/10/26 01:40:43 1.3 +++ /home/repository/moby/moby-live/Java/docs/Seahawk.html 2006/11/23 03:34:49 1.4 @@ -50,7 +50,7 @@

                                                                                  How do I launch it?

                                                                                  -

                                                                                  The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk/tt>

                                                                                  +

                                                                                  The applet can be launched from the following Web site: http://moby.ucalgary.ca/seahawk/. If you are a programmer, you can run it with a checked out version of the jMOBY CVS: ./build.sh seahawk

                                                                                  @@ -121,7 +121,7 @@
                                                                                  Paul Gordon
                                                                                  -Last modified: Thu Jul 6 14:24:53 MDT 2006 +Last modified: Wed Nov 22 20:32:48 MST 2006 From gordonp at dev.open-bio.org Thu Nov 23 19:28:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Nov 2006 14:28:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611231928.kANJSx2v024829@dev.open-bio.org> gordonp Thu Nov 23 14:28:59 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv24794/src/main/ca/ucalgary/seahawk/util Modified Files: MinJarMaker.java Log Message: Improvements to Minnow completeness (grabbing extra specified files to the JAR from file or other JARs) moby-live/Java/src/main/ca/ucalgary/seahawk/util MinJarMaker.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/11/01 23:45:36 1.2 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MinJarMaker.java 2006/11/23 19:28:58 1.3 @@ -5,6 +5,7 @@ import java.util.*; import java.util.jar.*; import java.net.URL; +import java.util.regex.Pattern; /** * This class should be called from the command line using a "clean" JVM @@ -51,7 +52,7 @@ // Check arguments if (args.length < 2) { System.err.println("Usage:\n\n"); - System.err.println("java -cp /dir/containing/only/the/MinJarMaker/class/file -Djarmaker.class.path=$CLASSPATH MinJarMaker main_output.jar [-s | -sw indexoutfile.xml] Program [args...]"); + System.err.println("java -cp /dir/containing/only/the/MinJarMaker/class/file -Djarmaker.class.extras=\"extra/classes/to/include.class\" -Djarmaker.class.path=$CLASSPATH MinJarMaker main_output.jar [-s | -sw indexoutfile.xml] Program [args...]"); System.err.println("Where -s causes the creation of secondary jar files for each package that doesn't"); System.err.println("have all of its classes loaded (i.e. may be loaded in further program execution)"); System.err.println("Where -sw also creates a Web Start document fragment describing the location of"); @@ -439,6 +440,147 @@ jout.closeEntry(); } + protected void addExtraClasses(Set classes){ + StringTokenizer extraClassesTokens = new StringTokenizer(System.getProperty("jarmaker.class.extras"), + File.pathSeparator); + while(extraClassesTokens.hasMoreElements()){ + String classPathElement = extraClassesTokens.nextToken(); + // A literal class to include, not a pattern + if(classPathElement.indexOf("*") == -1){ + byte[] classBytes = null; + try{ + classBytes = getClassBytes(classPathElement); + } + catch(Exception e){ + System.err.println("While trying to get extra class " + classPathElement); + e.printStackTrace(); + } + if(classBytes == null){ + System.err.println("Could not find the specified extra class: " + + classPathElement); + continue; + } + classes.add(classPathElement); + } + // A class pattern that we must find all matches for + else{ + Set matchedClasses = getMatchingClasses(classPathElement); + if(matchedClasses == null || matchedClasses.size() == 0){ + System.err.println("Could not find any classes matching the pattern specified for extra class: " + + classPathElement); + continue; + } + classes.addAll(matchedClasses); + } + } + } + + protected Set findDirMatches(String pathPrefix, File dir, Pattern p, boolean recursive){ + Set matches = new HashSet(); + + String[] files = dir.list(); + for(int i = 0; i < files.length; i++){ + if(files[i].indexOf(".") == 0){ + // skip hidden UNIX files, current dir, parent dir + continue; + } + File file = new File(dir, files[i]); + if(recursive && file.isDirectory()){ + matches.addAll(findDirMatches(pathPrefix, file, p, recursive)); + } + else if(p.matcher(files[i]).matches()){ + // This will mess up on windows, because the file separator \ will be an escape... + matches.add(file.getPath().replace(pathPrefix, "")); + } + } + + return matches; + } + + /** + * The pattern may have the form of an Ant path specification, i.e. "*" matches anything in a directory, + * and "**" matches anything in any subdirectory. + */ + protected Set getMatchingClasses(String pattern){ + Set results = new HashSet(); + + // This code largely copied from the getResourceURL method, with mods for asterisk handling + StringTokenizer classPathTokens = new StringTokenizer(System.getProperty("jarmaker.class.path"), + File.pathSeparator); + while(classPathTokens.hasMoreElements()){ + String pathElement = classPathTokens.nextToken(); + String path = pathElement + File.separator + pattern; + String parentPattern = ""; + if(pattern.indexOf(File.separator) != -1 && + pattern.indexOf(File.separator) != pattern.length()-1){ + parentPattern = pattern.substring(0, pattern.lastIndexOf(File.separator)+1); + } + + boolean recursive = false; + if(path.indexOf("**"+File.separator) != -1){ + recursive = true; + path = path.replaceAll("\\*\\*"+File.separator, ""); + parentPattern = parentPattern.replaceAll("\\*\\*"+File.separator, "(.*/)?"); + } + + File pathPattern = new File(path); + File pathParent = pathPattern.getParentFile(); + + // For now, we only take * or ** in the last part of the pattern + // (i.e. specific subdirectories cannot be specified after an asterisk, unless it's in a jar) + String patternWildcard = pathPattern.getName(); + // Turn the asterisked patterns into into regexs + if(patternWildcard.indexOf("**") != -1 && !recursive){ + recursive = true; + } + patternWildcard = patternWildcard.replaceAll("\\.", "\\\\."); // turn all periods into literal periods + patternWildcard = patternWildcard.replaceFirst("\\Q$\\E", "\\\\\\$"); // turn any $ into a literal one + patternWildcard = patternWildcard.replaceAll("\\*{1,2}", ".*"); + // Must match the entirety of the name (anchor start and end of regex + // to start and end of the file name to be compared to) + Pattern filep = Pattern.compile("^"+patternWildcard+"$"); + Pattern jarp = Pattern.compile("^"+parentPattern+ + (recursive ? "(.*/)?" : "") + + patternWildcard.replaceAll(File.separator, "/")+"$"); + + // The path exists in the file system + if(pathParent == null || pathParent.isDirectory()){ + results.addAll(findDirMatches(pathElement + File.separator, pathParent, filep, recursive)); + } + else{ + + // If it's not a valid file system path, 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; + } + + for(Enumeration entries = jarFile.entries(); entries.hasMoreElements();) { + JarEntry entry = entries.nextElement(); + if(jarp.matcher(entry.getName()).matches()){ + results.add(entry.getName()); + } + } + + try{ + jarFile.close(); + } + catch(IOException ioe){ + System.err.println("Couldn't close JAR file: " + pathElement); + } + } //end if file (jar) + } //end else if not dir + } //end for extra class path elements + return results; + } + protected void dumpJar( String jarfile ) throws IOException { // Get the list of classes @@ -447,6 +589,8 @@ corePackages = new Hashtable(); int partId = 1; //ID for part names in JNLP file (shorter than full package name to save space) + addExtraClasses(loadedClasses); + synchronized( loadedClasses ) { // Open up a new JAR file FileOutputStream fout = new FileOutputStream( jarfile ); From gordonp at dev.open-bio.org Thu Nov 23 19:28:59 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Thu, 23 Nov 2006 14:28:59 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611231928.kANJSxWA024847@dev.open-bio.org> gordonp Thu Nov 23 14:28:59 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv24794/xmls Modified Files: seahawkBuild.xml Log Message: Improvements to Minnow completeness (grabbing extra specified files to the JAR from file or other JARs) moby-live/Java/xmls seahawkBuild.xml,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/22 22:23:55 1.3 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/23 19:28:59 1.4 @@ -17,6 +17,7 @@ + @@ -55,10 +56,14 @@ + +
                                                                                  + +
                                                                                  From gordonp at dev.open-bio.org Fri Nov 24 20:54:17 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:54:17 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242054.kAOKsHHa028979@dev.open-bio.org> gordonp Fri Nov 24 15:54:16 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test In directory dev.open-bio.org:/tmp/cvs-serv28945/src/main/org/biomoby/service/test Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test added to the repository moby-live/Java/src/main/org/biomoby/service/test - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/RCS/directory,v: No such file or directory From gordonp at dev.open-bio.org Fri Nov 24 20:57:25 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:57:25 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242057.kAOKvPhp029043@dev.open-bio.org> gordonp Fri Nov 24 15:57:25 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv29008/src/main/ca/ucalgary/seahawk/gui Modified Files: MobyContentPane.java Log Message: Made namespace object retrieval simpler, and changed auth:service format for temp files to avoid invalid file names on Windows (':' isn't allowed in Windows file name apparently) moby-live/Java/src/main/ca/ucalgary/seahawk/gui MobyContentPane.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.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/gui/MobyContentPane.java 2006/10/25 02:33:22 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/MobyContentPane.java 2006/11/24 20:57:25 1.2 @@ -452,13 +452,17 @@ } private String serviceToFilePrefix(MobyService service){ - return service.getAuthority()+":"+service.getName()+":"; + return service.getAuthority()+"_SEAHAWk_"+service.getName()+"_SEAHAWk_"; } private MobyService filePrefixToService(String filename) throws Exception{ - StringTokenizer st = new StringTokenizer(filename, ":"); - String auth = st.nextToken(); - String name = st.nextToken(); + String tokens[] = filename.split("_SEAHAWk_"); + if(tokens == null || tokens.length < 2){ + return null; + } + + String auth = tokens[0]; + String name = tokens[1]; if(name == null){ return null; @@ -734,14 +738,7 @@ else{ mobyData = new MobyDataObject(""); } - MobyNamespace ns = new MobyNamespace(namespace); - try{ - ns.setDescription((String) servicesGUI.getMobyCentralImpl().getNamespaces().get(namespace)); - } - catch(MobyException mobye){ - logger.debug("Warning: can't retrieve namespace descriptions: " + mobye); - } - mobyData.addNamespace(ns); + mobyData.addNamespace(MobyNamespace.getNamespace(namespace)); if(mobyID != null){ mobyData.setId(mobyID); From gordonp at dev.open-bio.org Fri Nov 24 20:58:45 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:58:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242058.kAOKwjPj029103@dev.open-bio.org> gordonp Fri Nov 24 15:58:45 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv29072/src/main/ca/ucalgary/seahawk/util Added Files: SplashWindow.java Log Message: Added spalsh screen to application/applet jar of Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/util SplashWindow.java,NONE,1.1 From gordonp at dev.open-bio.org Fri Nov 24 20:58:45 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 15:58:45 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242058.kAOKwjrL029123@dev.open-bio.org> gordonp Fri Nov 24 15:58:45 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui In directory dev.open-bio.org:/tmp/cvs-serv29072/src/main/ca/ucalgary/seahawk/gui Modified Files: SeahawkSplasher.java Log Message: Added spalsh screen to application/applet jar of Seahawk moby-live/Java/src/main/ca/ucalgary/seahawk/gui SeahawkSplasher.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkSplasher.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/gui/SeahawkSplasher.java 2006/10/25 02:33:22 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/gui/SeahawkSplasher.java 2006/11/24 20:58:45 1.2 @@ -11,6 +11,7 @@ */ import javax.swing.JApplet; +import ca.ucalgary.seahawk.util.SplashWindow; /** * Modified to support both applet and application modes. From gordonp at dev.open-bio.org Fri Nov 24 21:10:39 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Fri, 24 Nov 2006 16:10:39 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611242110.kAOLAdlU029206@dev.open-bio.org> gordonp Fri Nov 24 16:10:39 EST 2006 Update of /home/repository/moby/moby-live/Java/xmls In directory dev.open-bio.org:/tmp/cvs-serv29171/xmls Modified Files: seahawkBuild.xml Log Message: Added ability to automatically deploy a signed applet (if you have a signing certificate, of course) moby-live/Java/xmls seahawkBuild.xml,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/23 19:28:59 1.4 +++ /home/repository/moby/moby-live/Java/xmls/seahawkBuild.xml 2006/11/24 21:10:39 1.5 @@ -2,16 +2,23 @@ + + + + - + + + + @@ -49,13 +56,16 @@ - + + + @@ -74,3 +84,56 @@ + + + + + + + + + + + + + + + +
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                                                                                  + + + + From gordonp at dev.open-bio.org Mon Nov 27 15:40:33 2006 From: gordonp at dev.open-bio.org (Paul Gordon) Date: Mon, 27 Nov 2006 10:40:33 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200611271540.kARFeXfb027537@dev.open-bio.org> gordonp Mon Nov 27 10:40:32 EST 2006 Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util In directory dev.open-bio.org:/tmp/cvs-serv27502/src/main/ca/ucalgary/seahawk/util Modified Files: SplashWindow.java Log Message: Fixed javadoc error moby-live/Java/src/main/ca/ucalgary/seahawk/util SplashWindow.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/SplashWindow.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/SplashWindow.java 2006/11/24 20:58:45 1.1 +++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/SplashWindow.java 2006/11/27 15:40:32 1.2 @@ -412,7 +412,7 @@ /** * Invokes the init method of the JApplet class provided by name. - * @param args the applet that was actually launched + * @param applet the applet that was actually launched */ public static void invokeInit(String className, javax.swing.JApplet applet) {