CDI and Guice with jsr-300 javax.inject In Same Webapp

Things can get weird when java SE code developed with IOC is deployed into a java EE container that implements CDI. For example - the littleware code I work with implements simple modules and life cycle management with guice, so when I deploy that code in a webapp to a glassfish server I want guice's runtime to manage littleware's dependency injection, but I might also want CDI to inject a glassfish-managed JPA EntityManager into a servlet for me, and both guice and CDI are scanning for the same javax.inject runtime annotations. Fortunately - this kind of thing worked fine for me until recently, since CDI 1 as introduced in java EE 6 ignored jars that did not include a META-INF/beans.xml file.

Java Enterprise Edition 6 introduced JSR-330 (javax.inject annotations and provider interfaces) and JSR-299 (CDI - contexts and dependency injection) to the java-ee platform. The javax.inject package standardized the annotations and interfaces used by java's various inversion of control and dependency-injection systems (guice, spring, dagger, pico container, ...), so that code written with one IOC system in mind could be more easily used in an application that deployed to another system.

CDI introduced an IOC implementation for java enterprise edition (EE) technologies (servlets, JSF, EJB, JPA, ...) deployed in EE containers like glassfish, jboss, weblogic, and websphere.

I discovered CDI's behavior changed slightly in the new java EE 7 runtime when a webapp that ran fine in glassfish version 3 (a java EE 6 container) failed to deploy under glassfish 4 (the EE-7 reference implementation). The errors in the glassfish-4 logs lead me to this ticket in guava's bug database. It turns out that CDI's new version 1.1 runtime automatically scans all jars deployed with an enterprise application, and guava-14+ includes a couple classes with javax.inject annotations that CDI processed in an unintended way (littleware still uses guice's com.google.inject package annotations and interfaces, so CDI ignored those).

I eventually found one easy solution to this javax.inject - CDI 1.1 mix-up is to add a META-INF/beans.xml CDI config file to jars that include javax.inject annotations that require special or no handling by CDI. I added the following META-INF/beans.xml with a bean-discover-mode attribute set to "none" to the guava jar in my webapp, and that solved the problem. Hopefully guava's maintainers will add a similar beans.xml file to guava's binary distribution on maven central.

<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
       bean-discovery-mode="none">
</beans>

javase Hibernate: goodbye Ejb3Configuration, hello JNDI Context mock

I've been cleaning up littleware's asset database code this week, and was dismayed to discover upon updating the hibernate dependencies that the latest hibernate releases have deprecated and removed the Ejb3Configuration mechanism for bootstrapping a JPA environment and allocating an EntityManagerFactory in a javase (no javaee container) application. Fortunately - I came up with a hacky way to trick hibernate into using the DataSource instance I want it to use.

Somehow when I started working with JPA I already had code in littleware's guice-based IOC setup to initialize and inject DataSource instances in traditional JDBC code either directly or via JNDI lookup. When I started using JPA in littleware I wanted to wire things up so that JPA used the same DataSource as the rest of the code. When running in a web container like Tomcat or Glassfish the app can let the container manage the DataSource, and both JPA and the guice-runtime access the same DataSource via a directory (JNDI) lookup, but when running a standalone application, I had things coded up to use hibernate, and used Ejb3Configuration to tell hibernate to use littleware's DataSource.

Anyway, with Ejb3Configuration going away I had to specify the database connection parameters in a JPA persistence.xml file in one of two ways. The first option was to specify properties for a JDBC Driver that JPA (hibernate) would wrap with its own connection pool manager, and the first hack I tried implemented a JDBC Driver (it's just a one method interface) that pulled connections from littleware's DataSource. That actually worked fine - I'm always amazed when these things work. I setup persistence.xml like this:

<?xml version="1.0" encoding="UTF-8"?>

<persistence xmlns="http://java.sun.com/xml/ns/persistence"
             xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
             xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
             version="2.0">

  <persistence-unit name="littlewarePU" transaction-type="RESOURCE_LOCAL">
        <description>This JPA persistence unit tracks littleware assets
        </description>

        <!-- jndi datasource lookup        
        <non-jta-data-source>jdbc/littleDB</non-jta-data-source>
        -->
        
        <class>littleware.asset.server.db.jpa.AssetTypeEntity</class>
        <class>littleware.asset.server.db.jpa.TransactionEntity</class>
        <class>littleware.asset.server.db.jpa.AssetAttribute</class>
        <class>littleware.asset.server.db.jpa.AssetDate</class>
        <class>littleware.asset.server.db.jpa.AssetLink</class>
        <class>littleware.asset.server.db.jpa.AssetEntity</class>

    <properties>

      <property name="eclipselink.target-database" value="DERBY"/>
      <property name="eclipselink.ddl-generation" value="create-tables" />
      <property name="hibernate.hbm2ddl.auto" value="create"/>
      <property name="hibernate.dialect" value="org.hibernate.dialect.DerbyDialect" />
            
      <property name="javax.persistence.jdbc.driver" value="littleware.asset.server.db.jpa.LittleDriver"/>
      <property name="javax.persistence.jdbc.url" value="jdbc:littleware://ignore/this/stuff"/>
      <property name="javax.persistence.jdbc.user" value="APP"/>
      <property name="javax.persistence.jdbc.password" value="APP"/>

    </properties> 
    
  </persistence-unit>
</persistence>

And I wrote a bogus littleware.asset.server.db.jpa.LittleDriver that some initialization code configured via its setDataSource() method:

/**
 * JDBC driver that just delegates to the active DataSource defined in the
 * active littleware runtime.
 * Register this driver with JPA persistence.xml to plug into the
 * littleware managed DataSource.
 */
public class LittleDriver implements Driver {
    private static  DataSource dataSource = null;
    /**
     * HibernateProvider injects littleware data source at startup time as needed
     */
    public static void setDataSource( DataSource value ) {
        dataSource = value;
    }
    
    
    @Override
    public Connection connect(String string, Properties prprts) throws SQLException {
        Whatever.get().check( "LittleDriver requires data source injection",  null != dataSource );
        return dataSource.getConnection();
    }

    @Override
    public boolean acceptsURL(String string) throws SQLException {
        return true;
    }

    private static final DriverPropertyInfo[] empty = new DriverPropertyInfo[0];
    @Override
    public DriverPropertyInfo[] getPropertyInfo(String string, Properties prprts) throws SQLException {
        return empty;
    }

    @Override
    public int getMajorVersion() {
        return 0;
    }

    @Override
    public int getMinorVersion() {
        return 0;
    }

    @Override
    public boolean jdbcCompliant() {
        return false;
    }

    private static final Logger log = Logger.getLogger( LittleDriver.class.getName() );
    @Override
    public Logger getParentLogger() throws SQLFeatureNotSupportedException {
        return log;
    }
    
}

Anyway - that worked great, and it's actually good enough for my current needs (mostly just junit tests), but it made me itch thinking about hibernate wrapping a connection pool around a mock driver that pulls connections from another connection pool. Ugh. So I started thinking about setting up an in-memory JNDI directory where initialization code could stuff the DataSource before allocating the JPA (hibernate or whatever) EntityManagerFactory. I found this cool little SimpleJNDI JNDI implementation, but it wasn't registered with Maven central, and it was a little bigger than I would like to copy into my code base, and anyway - I didn't need a whole JNDI implementation - I just needed to trick hibernate into using my DataSource, so I tried just wiring up a mock JNDI Context, and it worked! It took a few tries to figure out which methods hibernate calls to do its directory lookup, but in the end I wound up with a persistence.xml file like this:

<?xml version="1.0" encoding="UTF-8"?>

<persistence xmlns="http://java.sun.com/xml/ns/persistence"
             xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
             xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
             version="2.0">

  <persistence-unit name="littlewarePU" transaction-type="RESOURCE_LOCAL">
        <description>This JPA persistence unit tracks littleware assets
        </description>

        <non-jta-data-source>jdbc/littleDB</non-jta-data-source>
        
        <class>littleware.asset.server.db.jpa.AssetTypeEntity</class>
        <class>littleware.asset.server.db.jpa.TransactionEntity</class>
        <class>littleware.asset.server.db.jpa.AssetAttribute</class>
        <class>littleware.asset.server.db.jpa.AssetDate</class>
        <class>littleware.asset.server.db.jpa.AssetLink</class>
        <class>littleware.asset.server.db.jpa.AssetEntity</class>

    <properties>
    </properties> 
    
  </persistence-unit>
</persistence>

The mock JNDI Context looks like this:

/**
 * Mock JNDI context that is just NOOPs except
 * lookup always returns the DataSource injected via
 * the setDataSource static method.
 * Similar to LittleDriver - just a hack to try to get
 * hibernate to use our DataSource
 */
public class LittleContext implements javax.naming.Context {
    private static  DataSource dataSource = null;
    /**
     * HibernateProvider injects littleware data source at startup time as needed
     */
    public static void setDataSource( DataSource value ) {
        dataSource = value;
    }

    @Override
    public Object lookup(Name name) throws NamingException {
        return dataSource;
    }

    @Override
    public Object lookup(String string) throws NamingException {
        return dataSource;
    }

    @Override
    public void bind(Name name, Object o) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void bind(String string, Object o) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void rebind(Name name, Object o) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void rebind(String string, Object o) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void unbind(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void unbind(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void rename(Name name, Name name1) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void rename(String string, String string1) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public NamingEnumeration<NameClassPair> list(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public NamingEnumeration<NameClassPair> list(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public NamingEnumeration<Binding> listBindings(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public NamingEnumeration<Binding> listBindings(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void destroySubcontext(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void destroySubcontext(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Context createSubcontext(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Context createSubcontext(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Object lookupLink(Name name) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Object lookupLink(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public NameParser getNameParser(Name name) throws NamingException {
        return getNameParser("");
    }

    @Override
    public NameParser getNameParser( String string) throws NamingException {
        return new NameParser(){

            @Override
            public Name parse( final String string) throws NamingException {
                return new Name(){
                    @Override
                    public Object clone() { return this; }
                    
                    @Override
                    public int compareTo(Object o) {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public int size() {
                        return 1;
                    }

                    @Override
                    public boolean isEmpty() {
                        return false;
                    }

                    @Override
                    public Enumeration<String> getAll() {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public String get(int i) {
                        return string;
                    }

                    @Override
                    public Name getPrefix(int i) {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Name getSuffix(int i) {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public boolean startsWith(Name name) {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public boolean endsWith(Name name) {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Name addAll(Name name) throws InvalidNameException {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Name addAll(int i, Name name) throws InvalidNameException {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Name add(String string) throws InvalidNameException {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Name add(int i, String string) throws InvalidNameException {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }

                    @Override
                    public Object remove(int i) throws InvalidNameException {
                        throw new UnsupportedOperationException("Not supported yet."); 
                    }
                };

            }
        };
    }

    @Override
    public Name composeName(Name name, Name name1) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public String composeName(String string, String string1) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Object addToEnvironment(String string, Object o) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Object removeFromEnvironment(String string) throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public Hashtable<?, ?> getEnvironment() throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    @Override
    public void close() throws NamingException {}

    @Override
    public String getNameInNamespace() throws NamingException {
        throw new UnsupportedOperationException("Not supported yet."); 
    }

    
    //---------------------------
    
    /**
     * Assign this to the "java.naming.factory.initial" system property
     * to make the LittleContext mock the initial context.
     */
    public static class Factory implements javax.naming.spi.InitialContextFactory {

        @Override
        public Context getInitialContext(Hashtable<?, ?> hshtbl) throws NamingException {
            return new LittleContext();
        }
        
    }
}

This is the JPA EntityManager guice Provider used in a standalone application:

@Singleton
public class HibernateProvider implements Provider<EntityManagerFactory> {

    private final DataSource dataSource;
    private final String dataSourceURL;
    private EntityManagerFactory emFactory = null;


    @Inject
    public HibernateProvider(@Named("datasource.littleware") DataSource dsource,
            @Named("datasource.littleware") String sDatasourceUrl) {
        dataSource = dsource;
        dataSourceURL = sDatasourceUrl;
    }


    @Override
    public EntityManagerFactory get() {
        if (null == emFactory) {
            LittleDriver.setDataSource( dataSource );
            LittleContext.setDataSource( dataSource );
            if ( null == System.getProperty(  "java.naming.factory.initial" ) ) {
                System.setProperty( "java.naming.factory.initial", LittleContext.Factory.class.getName() );
            }
            
            emFactory = Persistence.createEntityManagerFactory( "littlewarePU" );
        }
        return emFactory;
    }
}

Anyway - I barely know how to use JPA, so duplicate these hacks at your own risk. The code is online here for now (I'm always moving things around in that repo).

typescript syntax highlighting in jedit and netbeans

Typescript syntax-highlighting is available in a few editors (vim, emacs, sublime) thanks to editor plugins published by Microsoft, and deeper type-aware language support with code-completion and refactoring is available for Visual Studio. Of course the code editors I usually use (jedit and netbeans) don't include typescript support, so I took a little time to see if I could get something working.

Adding basic typescipt support to jedit was easy. JEdit's syntax highlighting and indentation logic for a particular file is driven by the "mode" xml file associated with the file's extension (.js, .ts, .java, whatever). JEdit extracts lexical rules for syntax-coloring from the lists of keywords, operators, and regular expressions in the mode file. For typescript I associated .ts files with jedit's javascript mode, and added a few items to the keyword lists in javascript's mode xml file (declare, export, ...), and I was pretty happy with the result. This thread on stackoverflow describes where to find mode xml files, and the mode "catalog" file. I also disabled the typoscript (European CMS - who knew?) entry in the catalog, because typoscript also uses the ".ts" file extension:

<MODE NAME="javascript"  FILE="javascript.xml"
    FILE_NAME_GLOB="{*.{js,ts},Buildsub}" />

...
<MODE NAME="typoscript"  FILE="typoscript.xml"
    FILE_NAME_GLOB="*.tsXXX"/<

I tried a similar trick with netbeans, and followed these instructions to configure netbeans to treat ".ts" files as javascript. Unfortunately the resulting behavior in a netbeans editor is not that great. Netbeans builds its language support around a parser of the full language grammar - it doesn't just highlight keywords. The various syntax structures in typescript that are not legal in javascript are highlighted as errors in netbeans. Ugh! Anyway - it's better than nothing. This page has instructions for coding in java a netbeans module for a new language. It would be a fun project to code up a typescript extension for netbeans using the typescript tsc compiler via the java-based rhino javascript engine. This entry describes running tsc with rhino on the command line. I'll save that project for another day ...

compiling typescript with rhino javascript engine

I spent way too long the last couple days patching the typescript compiler (tsc) to run with java's rhino javascript engine. I mentioned in an earlier post how my dell laptop died on me. I wound up buying an hp envy m4 laptop on clearance at BestBuy to replace it, but before that I did that I was goofing around for a couple days getting by with my Android phone and the old PowerBook G4 I pulled off the shelf that amazingly boot up for me. Anyway - I thought I'd try to get tsc running from the command-line. The compiler is javascript compiled from typescript code, so I first tried to build node from source, but node's build setup requires newer versions of python, make, and gcc than what the powerbook had, so then I got the idea to try to run tsc with rhino, since the powerbook did have java 1.5 installed (java 1.6+ ships with rhino and a jrunscript command line tool). Of course it didn't "just work", and I let myself get sucked into banging my head on it - even after I got the new laptop. Ugh.

Anyway - I eventually got tsc running with rhino (the patch listing is further below). The easy part of the project was implementing a rhino version of tsc's IIO interface for file IO. The rhino implementation just calls through to java.io classes, and tsc runs a few feature tests to figure out which javascript engine it's running under:

    if (typeof ActiveXObject === "function")
        return getWindowsScriptHostIO();
    else if (typeof require === "function")
        return getNodeIO();
    else if ( typeof java != "undefined" )
        return getRhinoIO();
    else
        return null; // Unsupported host

The IO code was straight forward; the painful part was working around rhino's quirks. The first quirk I ran into was that rhino appears to treat the names of java's primitive types as reserved words, so things like:
var byte = 0;
or option.short = "v";
are illegal. Fortunately - that only popped up a couple places in the tsc code, but it's an unfortunate "feature" for rhino to have.

Another problem I ran into was invoking "delete" on an instance of java.io.File. Javascript includes delete in its collection of reserved words, but it should be legal to include a "delete()" method on some class. Rhino's javascript grammar probably just needs some love. The workaround was to access the method via f["delete"]() instead of f.delete().

C:\Users\Reuben\Documents\Code\typescript\src\compiler
> node
> var Foo = function() { return this; }
undefined
> Foo.prototype.delete = function() { return "bla"; }
[Function]
> (new Foo()).delete();
'bla'

...


> C:\Users\Reuben\Documents\Code\typescript\src\compiler
> jrunscript
js> var Foo = function() { return this; }
js> Foo.prototype.delete = function() { return "bla"; }
script error: sun.org.mozilla.javascript.internal.EvaluatorException: missing name after . operator (<STN> at line number 1
js>

Another problematic feature of rhino is that it does not hide the distinction between javascript's string type (which tsc expects), and java's java.lang.String. I discovered that Rhino has methods for converting between java types and javascript types - including the String() method mentioned here:

    resolvePath: function (path) {
        return <string> String( (new java.io.File(path)).getCanonicalPath() );
    },

There were one or two other small rhino quirks to work out, but the big one that surprised me was that rhino's regular expression objects apparently don't respect javascript's normal scoping rules. The tsc compiler was failing under rhino with various undefined types that weren't properly pulled in via the file-reference comments (see section 9.1.1 in the typescript spec). I eventually had a test setup, and found rhino would load every other referenced file, so a tsc run with rhino had this output:

(1)Reading code from C:/Users/Reuben/Documents/Code/typescript/src/compiler/typescript.ts
Found code at C:/Users/Reuben/Documents/Code/typescript/src/compiler/typescript.ts
 file reference: diagnostics.ts
 file reference: nodeTypes.ts
 file reference: ast.ts
 file reference: astWalkerCallback.ts
 file reference: astLogger.ts
 file reference: base64.ts
 file reference: emitter.ts
 file reference: parser.ts
 file reference: scanner.ts
 file reference: scopeWalk.ts
 file reference: symbols.ts
 file reference: tokens.ts
 file reference: typeCollection.ts
 file reference: types.ts
 file reference: referenceResolution.ts
 file reference: incrementalParser.ts

The output with nodejs was:

   (1)Reading code from C:/Users/Reuben/Documents/Code/typescript/src/compiler/typescript.ts
   Found code at C:/Users/Reuben/Documents/Code/typescript/src/compiler/typescript.ts
    file reference: diagnostics.ts
    file reference: flags.ts
    file reference: nodeTypes.ts
    file reference: hashTable.ts
    file reference: ast.ts
    file reference: astWalker.ts
    file reference: astWalkerCallback.ts
    file reference: astPath.ts
    file reference: astLogger.ts
    file reference: binder.ts
    file reference: base64.ts
    file reference: sourceMapping.ts
    file reference: emitter.ts
    file reference: errorReporter.ts
    file reference: parser.ts
    file reference: printContext.ts
    file reference: scanner.ts
    file reference: scopeAssignment.ts
    file reference: scopeWalk.ts
    file reference: signatures.ts
    file reference: symbols.ts
    file reference: symbolScope.ts
    file reference: tokens.ts
    file reference: typeChecker.ts
    file reference: typeCollection.ts
    file reference: typeFlow.ts
    file reference: types.ts
    file reference: pathUtils.ts
    file reference: referenceResolution.ts
    file reference: precompile.ts
    file reference: incrementalParser.ts
    file reference: declarationEmitter.ts

Anyway, long story short, it turned out that the reference strings were each processed by a function with a regular expression, and rhino had this crazy behavior where regular expression objects appear to be global.

with rhino:

js> function doTest( s ) { var rx =  /^\s*(\/\/\/\s*/gim;
return (rx.exec(s) == null); }

js> doTest(comment);
false
js> doTest(comment);
true
js> doTest(comment);
false
js> doTest(comment);
true

with node:
> function doTest(s) {
... var rx =  /^\s*(\/\/\/\s*/gim;
... return (rx.exec(s) == null);
... }
undefined
> comment
'///<reference path=\'sourceMapping.ts\' />'
> doTest(comment);
false
> doTest(comment);
false
> doTest(comment);
false
> doTest(comment);
false
> doTest(comment);
false

Unbelievable. Anyway - the work around is to reset the rx.lastIndex before each run, so:

    function getFileReferenceFromReferencePath(comment: string): IFileReference {
        var referencesRegEx = /^(\/\/\/\s*<reference\s+path=)('|")(.+?)\2\s*(static=('|")(.+?)\2\s*)*\/>/gim;
        referencesRegEx.lastIndex = 0;  // work around ridiculous bug in rhino ...
        var match = referencesRegEx.exec(comment);
        ...

Finally - I just tested this stuff by running the compiler on itself. The typescript repo on codeplex includes a bunch of test cases and an nmake based Makefile, but I was too lazy to download visual studio and get that working. In the end - rhino compiled tsc in 2 minutes, and node did it in 3 seconds. Ugh!

C:\Users\Reuben\Documents\Code\typescript\src\compiler
> date; jrunscript tsc.js --out tsc2.js tsc.ts; date

Monday, June 3, 2013 12:49:41 PM
Monday, June 3, 2013 12:51:39 PM


C:\Users\Reuben\Documents\Code\typescript\src\compiler
> date; node tsc2.js --out tsc3.js tsc.ts; date

Monday, June 3, 2013 12:58:40 PM
Monday, June 3, 2013 12:58:43 PM

Update 2013/06/29: I tried java 8's new nashorn javascript engine (in a jdk8 pre-release) to see how it did. Nashorn currently runs the tsc compile about 10% faster than rhino - still a lot slower than node. Doh!

> date; & 'C:\Program Files\Java\jdk1.8.0\bin\jrunscript.exe' .\tsc2.js --out tsc2.js tsc.ts; date;

Saturday, June 29, 2013 5:29:11 PM
Saturday, June 29, 2013 5:30:57 PM

Anyway - I'll check to see if the typescript maintainers will accept this patch, but I'll be surprised if they want anything to do with rhino after reading this sad tale ...

diff --git a/src/compiler/base64.ts b/src/compiler/base64.ts
index ee2d3c5..b4fc315 100644
--- a/src/compiler/base64.ts
+++ b/src/compiler/base64.ts
@@ -67,20 +67,21 @@ module TypeScript {
 
             var shift = 0;
             for (var i = 0; i < inString.length; i++) {
-                var byte = Base64Format.decodeChar(inString[i]);
+                // note: "byte" is reserved in java Rhino javascript environment - ugh
+                var bite = Base64Format.decodeChar(inString[i]);
                 if (i === 0) {
                     // Sign bit appears in the LSBit of the first value
-                    if ((byte & 1) === 1) {
+                    if ((bite & 1) === 1) {
                         negative = true;
                     }
-                    result = (byte >> 1) & 15; // 1111x
+                    result = (bite >> 1) & 15; // 1111x
                 } else {
-                    result = result | ((byte & 31) << shift); // 11111
+                    result = result | ((bite & 31) << shift); // 11111
                 }
 
                 shift += (i == 0) ? 4 : 5;
 
-                if ((byte & 32) === 32) {
+                if ((bite & 32) === 32) {
                     // Continue
                 } else {
                     return { value: negative ? -(result) : result, rest: inString.substr(i + 1) };
diff --git a/src/compiler/io.ts b/src/compiler/io.ts
index a5eb1ad..6e75bf2 100644
--- a/src/compiler/io.ts
+++ b/src/compiler/io.ts
@@ -13,6 +13,9 @@
 // limitations under the License.
 //
 
+declare var arguments:any;
+var javaArgs:any = arguments; // Rhino sets global arguments ... bla
+
 interface IResolvedFile {
     content: string;
     path: string;
@@ -105,7 +108,10 @@ declare class Enumerator {
     constructor (o: any);
 }
 declare function setTimeout(callback: () =>void , ms?: number);
+
 declare var require: any;
+declare var java: any;
+
 declare module process {
     export var argv: string[];
     export var platform: string;
@@ -123,7 +129,7 @@ declare module process {
 }
 
 var IO = (function() {
-
+    
     // Create an IO object for use inside WindowsScriptHost hosts
     // Depends on WSCript and FileSystemObject
     function getWindowsScriptHostIO(): IIO {
@@ -533,12 +539,251 @@ var IO = (function() {
             },
             quit: process.exit
         }
-    };
+    }
+    ;
+        
+    
+    function getRhinoIO():IIO {
+        var utf8 = java.nio.charset.Charset.forName( "UTF-8" );
+        var jscriptArgs = [];
+   
+        for( var i=0; i < javaArgs.length; ++i ) {
+            //
+            // convert java string to javascript string (so javascript string methods work - ugh!)
+            // see https://groups.google.com/forum/?fromgroups#!topic/mozilla.dev.tech.js-engine.rhino/FV15_KJVLGM
+            //
+            jscriptArgs.push( String( javaArgs[i] ) );
+        }
+        
+        
+        /**
+         * Byte-order-mark detector - ugh.
+         * @param streamInn java.io.InputStream
+         * @return java.io.Reader
+         * @see http://blog.publicobject.com/2010/08/handling-byte-order-mark-in-java.html
+         */
+       function inputStreamToReader(streamIn) {
+         // buffered stream supports mark and reset
+         var stream = new java.io.BufferedInputStream( streamIn );
+         stream.mark(3);
+         var byte1 = stream.read();
+         var byte2 = stream.read();
+         if (byte1 == 0xFF && byte2 == 0xFE) {
+           return new java.io.InputStreamReader(stream, "UTF-16LE");
+         } else if (byte1 == 0xFF && byte2 == 0xFF) {
+           return new java.io.InputStreamReader(stream, "UTF-16BE");
+         } else {
+           var byte3 = stream.read();
+           if (byte1 == 0xEF && byte2 == 0xBB && byte3 == 0xBF) {
+             return new java.io.InputStreamReader(stream, "UTF-8");
+           } else {
+             stream.reset();
+             return new java.io.InputStreamReader(stream);
+           }
+         }
+       };
+
+          return {
+            readFile: function (file):string {
+                try  {
+                    var f = new java.io.File( file );
+                    if( (! f.exists()) || (! f.isFile()) ) { return ""; }
+                    var buffer = java.lang.reflect.Array.newInstance( java.lang.Character.TYPE, f.length() + 128 ); // 128 fudge
+                    var reader = new java.io.BufferedReader( 
+                       inputStreamToReader(
+                              new java.io.FileInputStream( f ) 
+                         ) 
+                    );
+                    try {
+                     var offset = 0;
+                        for( var step = reader.read( buffer, offset, buffer.length - offset ); 
+                             step >= 0; step = reader.read( buffer, offset, buffer.length - offset ) ) {
+                             offset += step;
+                             //java.lang.System.out.println( "Just read num bytes: " + step );
+                        }
+                        var javaString = new java.lang.String( buffer, 0, offset )
+                        //java.lang.System.out.println( "Read: " + javaString );
+                        // convert java string to javascript string ... ugh
+                        return <string> String( new java.lang.String( buffer, 0, offset ) );
+                    } catch (ex) { 
+                        reader.close();
+                        ex.printStackTrace( java.lang.System.err );
+                        throw ex; 
+                    }
+                } catch (e) {
+                    IOUtils.throwIOError("Error reading file \"" + file + "\" - " + e.toString(), e );
+                }
+            },
+            writeFile: function( path, content ) {
+               var f = new java.io.File( path );
+               if( f.exists() && f.isFile() ) {
+                   var writer = new java.io.OutputStreamWriter(
+                         new java.io.FileOutputStream( f ), utf8
+                    );
+                    writer.write( content );
+                    writer.close();
+               }
+            },
+            deleteFile: function (path) {
+               var f = new java.io.File( path );
+               if( f.exists() && f.isFile() ) {
+                   // delete is reserved in javascript - confused Rhino parser - ugh
+                   f["delete"]();
+                }
+            },
+            fileExists: function (path) {
+                var result:bool = (new java.io.File( path )).exists();
+                return result;
+            },
+            createFile: function (path, useUTF8?) {
+                var f = new java.io.File( path );
+                if ( f.exists() && (! f.isFile()) ) {
+                    IOUtils.throwIOError("Error creating file \"" + path + "\".", null ); 
+                } else if ( ! f.exists() ) {
+                    var dir = f.getParentFile();
+                    dir.mkdirs();
+                }
+                try  {
+                    var writer = new java.io.OutputStreamWriter(
+                             new java.io.FileOutputStream( f ), utf8
+                            );
+                } catch (e) {
+                    IOUtils.throwIOError("Couldn't write to file '" + path + "'.", e);
+                }
+                return new IOUtils.BufferedTextWriter( {
+                    Write: function (str:string ) {
+                        writer.write( str );
+                    },
+                    WriteLine: function (str:string) {
+                        writer.write( str + "\n" );
+                    },
+                    Close: function () {
+                        writer.close();
+                        writer = null;
+                    }
+                } );
+            },
+            dir: function dir(path, spec?, options?):string[] {
+                options = options || {
+                };
+                function filesInFolder(folder:any):string[] {
+                    var paths = [];
+                    var files = folder.listFiles();
+                    for(var i = 0; i < files.length; i++) {
+                        var f = files[i];
+                        if(options.recursive && f.isDirectory()) {
+                            paths = paths.concat(filesInFolder(f));
+                        } else if(f.isFile() && (!spec || f.getName().match(spec))) {
+                            paths.push( String( f.getPath() ) ); // convert to javascript String
+                        }
+                    }
+                    return paths;
+                }
+                return filesInFolder( new java.io.File( path ) );
+            },
+            createDirectory: function (path) {
+                try  {
+                    if(!this.directoryExists(path)) {
+                       (new java.io.File( path )).mkdirs();
+                    }
+                } catch (e) {
+                    IOUtils.throwIOError("Couldn't create directory '" + path + "'.", e);
+                }
+            },
+            directoryExists: function (path) {
+                var f = new java.io.File( path );
+                var result:bool = f.exists() && f.isDirectory();
+                return result;
+            },
+            resolvePath: function (path) {
+                return <string> String( (new java.io.File(path)).getCanonicalPath() );
+            },
+            dirName: function (path) {
+                return <string> String( (new java.io.File( path )).getCanonicalFile().getParent() );
+            },
+            findFile: function (rootPath, partialFilePath) {
+                var scan = new java.io.File( rootPath + "/" + partialFilePath ).getCanonicalFile();
+                while(true) {
+                    if( scan.exists() ) {
+                        try  {
+                            var content = this.readFile( scan.getPath() );
+                            return {
+                                content: <string> content,
+                                path: <string> String( scan.getPath() )
+                            };
+                        } catch (err) {
+                        }
+                    } else {
+                        // climb up the file system ... ?
+                        var parent = (new java.io.File( rootPath )).getParent();
+                        if( parent == null ) {
+                            return null;
+                        } else {
+                            scan = new java.io.File( parent, partialFilePath );
+                        }
+                    }
+                }
+            },
+            print: function (str) {
+                java.lang.System.out.print( str );
+            },
+            printLine: function (str) {
+                java.lang.System.out.println( str );
+            },
+            arguments: <string[]> jscriptArgs, 
+            stderr: {
+                Write: function (str) {
+                    java.lang.System.err.print(str);
+                },
+                WriteLine: function (str) {
+                    java.lang.System.err.println(str );
+                },
+                Close: function () {
+                }
+            },
+            stdout: {
+                Write: function (str) {
+                    java.lang.System.out.print(str);
+                },
+                WriteLine: function (str) {
+                    java.lang.System.out.println(str );
+                },
+                Close: function () {
+                }
+            },
+            
+            /**
+             * Could implement watchFile() with java-7 nio2 code, but too lazy to bother,
+             * since WindowsScriptHost skips this method too ... :)
+             * @see http://docs.oracle.com/javase/tutorial/essential/io/notification.html 
+             */
+            watchFile: null,
+            run: function(source, filename) {
+                try {
+                    eval(source);
+                } catch (e) {
+                    IOUtils.throwIOError("Error while executing file '" + filename + "'.", e);
+                }
+            },
+            getExecutingFilePath: function () {
+                return this.arguments[0];
+            },
+            quit: function (exitCode? : number = 0) {
+                try {
+                    java.lang.System.lang.exit(exitCode);
+                } catch (e) {
+                }
+            }
+        };
+    }
+    ;
 
     if (typeof ActiveXObject === "function")
         return getWindowsScriptHostIO();
     else if (typeof require === "function")
         return getNodeIO();
+    else if ( typeof java != "undefined" )
+        return getRhinoIO();
     else
         return null; // Unsupported host
 })();
diff --git a/src/compiler/optionsParser.ts b/src/compiler/optionsParser.ts
index a10fb8f..7a7eb73 100644
--- a/src/compiler/optionsParser.ts
+++ b/src/compiler/optionsParser.ts
@@ -18,7 +18,7 @@
 interface IOptions {
     name?: string;
     flag?: bool;
-    short?: string;
+    shorty?: string;  // note: "short" is reserved in java
     usage?: string;
     set?: (s: string) => void;
     type?: string;
@@ -34,7 +34,7 @@ class OptionsParser {
 
         for (var i = 0; i < this.options.length; i++) {
 
-            if (arg === this.options[i].short || arg === this.options[i].name) {
+            if (arg === this.options[i].shorty || arg === this.options[i].name) {
                 return this.options[i];
             }
         }
@@ -89,8 +89,8 @@ class OptionsParser {
             var usageString = "  ";
             var type = option.type ? " " + option.type.toUpperCase() : "";
 
-            if (option.short) {
-                usageString += this.DEFAULT_SHORT_FLAG + option.short + type + ", ";
+            if (option.shorty) {
+                usageString += this.DEFAULT_SHORT_FLAG + option.shorty + type + ", ";
             }
 
             usageString += this.DEFAULT_LONG_FLAG + option.name + type;
@@ -110,27 +110,27 @@ class OptionsParser {
         }
     }
 
-    public option(name: string, config: IOptions, short?: string) {
+    public option(name: string, config: IOptions, shorty?: string) {
         if (!config) {
-            config = <any>short;
-            short = null;
+            config = <any>shorty;
+            shorty = null;
         }
 
         config.name = name;
-        config.short = short;
+        config.shorty = shorty;
         config.flag = false;
 
         this.options.push(config);
     }
 
-    public flag(name: string, config: IOptions, short?: string) {
+    public flag(name: string, config: IOptions, shorty?: string) {
         if (!config) {
-            config = <any>short;
-            short = null;
+            config = <any>shorty;
+            shorty = null;
         }
 
         config.name = name;
-        config.short = short;
+        config.shorty = shorty;
         config.flag = true
 
         this.options.push(config);
diff --git a/src/compiler/precompile.ts b/src/compiler/precompile.ts
index 88adf32..c66f937 100644
--- a/src/compiler/precompile.ts
+++ b/src/compiler/precompile.ts
@@ -131,6 +131,7 @@ module TypeScript {
 
     function getFileReferenceFromReferencePath(comment: string): IFileReference {
         var referencesRegEx = /^(\/\/\/\s*<reference\s+path=)('|")(.+?)\2\s*(static=('|")(.+?)\2\s*)*\/>/gim;
+        referencesRegEx.lastIndex = 0;  // work around ridiculous bug in rhino ...
         var match = referencesRegEx.exec(comment);
 
         if (match) {
@@ -294,6 +295,7 @@ module TypeScript {
             
             if (!comment.isBlock) {
                 var referencedCode = getFileReferenceFromReferencePath(comment.getText());
+                //CompilerDiagnostics.debugPrint( "Considering comment as possible reference (" + (referencedCode ? "ok" : "no") + "): " + comment.getText() );
                 if (referencedCode) {
                     referencedCode.minChar = comment.startPos;
                     referencedCode.limChar = referencedCode.minChar + comment.value.length;
diff --git a/src/compiler/referenceResolution.ts b/src/compiler/referenceResolution.ts
index 442d8ec..52ae47c 100644
--- a/src/compiler/referenceResolution.ts
+++ b/src/compiler/referenceResolution.ts
@@ -102,7 +102,7 @@ module TypeScript {
                 // if the path is relative, or came from a reference tag, we don't perform a search
                 if (isRelativePath || isRootedPath || !performSearch) {
                     try {
-                        CompilerDiagnostics.debugPrint("   Reading code from " + normalizedPath);
+                        CompilerDiagnostics.debugPrint("   (1)Reading code from " + normalizedPath);
                             
                         // Look for the .ts file first - if not present, use the .ts, the .d.str and the .d.ts
                         try {
@@ -116,19 +116,19 @@ module TypeScript {
                                 else if (isTSFile(normalizedPath)) {
                                     normalizedPath = changePathToSTR(normalizedPath);
                                 }
-                                CompilerDiagnostics.debugPrint("   Reading code from " + normalizedPath);
+                                CompilerDiagnostics.debugPrint("   (2)Reading code from " + normalizedPath);
                                 resolvedFile.content = ioHost.readFile(normalizedPath);
                             }
                             catch (err) {
                                 normalizedPath = changePathToDSTR(normalizedPath);
-                                CompilerDiagnostics.debugPrint("   Reading code from " + normalizedPath);
+                                CompilerDiagnostics.debugPrint("   (3)Reading code from " + normalizedPath);
 
                                 try {
                                     resolvedFile.content = ioHost.readFile(normalizedPath);
                                 }
                                 catch (err) {
                                     normalizedPath = changePathToDTS(normalizedPath);
-                                    CompilerDiagnostics.debugPrint("   Reading code from " + normalizedPath);
+                                    CompilerDiagnostics.debugPrint("   (4)Reading code from " + normalizedPath);
                                     resolvedFile.content = ioHost.readFile(normalizedPath);
                                 }
                             }
@@ -148,7 +148,10 @@ module TypeScript {
 
                     // if the path is non-relative, we should attempt to search on the relative path
                     resolvedFile = ioHost.findFile(parentPath, normalizedPath);
-
+                    CompilerDiagnostics.debugPrint("   Attempting to resolve (" + parentPath + ", " + normalizedPath + ") got: " + 
+                         (resolvedFile == null) ? "null" : resolvedFile.path 
+                    );
+                    
                     if (!resolvedFile) {
                         if (isSTRFile(normalizedPath)) {
                             normalizedPath = changePathToTS(normalizedPath);
@@ -187,6 +190,10 @@ module TypeScript {
                     var resolvedFilePath = ioHost.resolvePath(resolvedFile.path);
                     sourceUnit.referencedFiles = preProcessedFileInfo.referencedFiles;
 
+                    for (var i = 0; i < preProcessedFileInfo.referencedFiles.length; i++) {
+                        var fileReference = preProcessedFileInfo.referencedFiles[i];
+                        CompilerDiagnostics.debugPrint("    file reference: " + fileReference.path);
+                    }
                     // resolve explicit references
                     for (var i = 0; i < preProcessedFileInfo.referencedFiles.length; i++) {
                         var fileReference = preProcessedFileInfo.referencedFiles[i];