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MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.

XApi is a dependency injection, service-oriented, polyglot java framework. It is comprised of standalone modules for use in web, desktop and mobile java applications. This codebase enables complete reuse of all code across your java stack, as well as the ability to easily define your own Platform, so you can build your own customized runtime environment to extend or replace existing platforms. It is currently geared towards servlets and gwt clients, but the target we are currently developing include: java, gwt [webkit, firefox, ie], javafx, playn [android, ios, flash], appengine & vert.x For Google Web Toolkit, we also include reflection support, more complete emulation of java.lang.Class, zero-overhead dependency injection, a range of code generation utilities, and even "magic-method injection" (for production compiles any method in the app can be swapped out with others based on configuration properties, or any AST mangling / code generating methods you wish to write). There is also a bytecode transformer in the works which will replace calls into the DI utility with direct references to static final factories, to allow the java compiler to completely erase all injection overhead in all java runtimes.

Jadex Rules is a small lightweight rule engine, which currently employs the well-known Rete algorithm for highly efficient rule matching. Jadex rules is therefore similar to other rule engines like JESS and Drools. Despite the similarities there are also important differences between these systems: * Jadex Rules is very small and intended to be used as component of other software. Even though rules can be specified in a Java dialect as well as (a small variation of) the CLIPS language its primary usage is on the API level. Jadex Rules is currently the core component of the Jadex BDI reasoning engine. * Jadex Rules cleanly separates between state and rule representation. This allows the state implementation as well as the matcher to be flexibly exchanged. Some experiments have e.g. been conducted with a Jena representation. Regarding the matcher, it is planned to support also the Treat algorithm, which has a lower memory footprint than Rete. * Jadex Rules pays close attention to rule debugging. The state as well as the rete engine can be observed at runtime. The rule debugger provides functionalities to execute a rule program stepwise and also use rule breakpoints to stop the execution at those points.

This project aims to build a command line tool that can create HTML view with syntax highlighted source code. It uses Jedit syntax highlighting engine and support all languages that are supported in JEdit. Which are currently: ActionScript, Ada 95, ANTLR, Apache HTTPD, APDL, AppleScript, ASP, Aspect-J, Assembly, AWK, B formal method, Batch, BBj, BCEL, BibTeX, C, C++, C#, CHILL, CIL, COBOL, ColdFusion, CSS, CVS Commit, D, DOxygen, DSSSL, Eiffel, EmbPerl, Erlang, Factor, Fortran, Foxpro, FreeMarker, Fortran, Gettext, Groovy, Haskell, HTML, Icon, IDL, Inform, INI, Inno Setup, Informix 4GL, Interlis, Io, Java, JavaScript, JCL, JHTML, JMK, JSP, Latex, Lilypond, Lisp, LOTOS, Lua, Makefile, Maple, ML, Modula-3, MoinMoin, MQSC, NetRexx, NQC, NSIS2, Objective C, ObjectRexx, Occam, Omnimark, Parrot, Pascal, Patch, Perl, PHP, Pike, PL-SQL, PL/I, Pop11, PostScript, Povray, PowerDynamo, Progress 4GL, Prolog, Properties, PSP, PV-WAVE, Pyrex, Python, REBOL, Redcode, Relax-NG, RelationalView, Rest, Rib, RPM spec, RTF, Ruby, Ruby-HTML, RView, S+, S#, SAS, Scheme, SDL/PL, SGML, Shell Script, SHTML, Smalltalk, SMI MIB, SQR, Squidconf, SVN Commit, Swig, TCL, TeX, Texinfo, TPL, Transact-SQL, UnrealScript, VBScript, Velocity, Verilog, VHDL, XML, XSL, ZPT

Apache Commons Crypto is a cryptographic library optimized with AES-NI (Advanced Encryption Standard New Instructions). It provides Java API for both cipher level and Java stream level. Developers can use it to implement high performance AES encryption/decryption with the minimum code and effort. Please note that Crypto doesn't implement the cryptographic algorithm such as AES directly. It wraps to OpenSSL or JCE which implement the algorithms. Features -------- 1. Cipher API for low level cryptographic operations. 2. Java stream API (CryptoInputStream/CryptoOutputStream) for high level stream encryption/decryption. 3. Both optimized with high performance AES encryption/decryption. (1400 MB/s - 1700 MB/s throughput in modern Xeon processors). 4. JNI-based implementation to achieve comparable performance to the native C/C++ version based on OpenSsl. 5. Portable across various operating systems (currently only Linux/MacOSX/Windows); Apache Commons Crypto loads the library according to your machine environment (it checks system properties, `os.name` and `os.arch`). 6. Simple usage. Add the commons-crypto-(version).jar file to your classpath. Export restrictions ------------------- This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software. BEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. See <http://www.wassenaar.org/> for more information. The U.S. Government Department of Commerce, Bureau of Industry and Security (BIS), has classified this software as Export Commodity Control Number (ECCN) 5D002.C.1, which includes information security software using or performing cryptographic functions with asymmetric algorithms. The form and manner of this Apache Software Foundation distribution makes it eligible for export under the License Exception ENC Technology Software Unrestricted (TSU) exception (see the BIS Export Administration Regulations, Section 740.13) for both object code and source code. The following provides more details on the included cryptographic software: * Commons Crypto use [Java Cryptography Extension](http://docs.oracle.com/javase/8/docs/technotes/guides/security/crypto/CryptoSpec.html) provided by Java * Commons Crypto link to and use [OpenSSL](https://www.openssl.org/) ciphers

Mahout's goal is to build scalable machine learning libraries. With scalable we mean: Scalable to reasonably large data sets. Our core algorithms for clustering, classification and batch based collaborative filtering are implemented on top of Apache Hadoop using the map/reduce paradigm. However we do not restrict contributions to Hadoop based implementations: Contributions that run on a single node or on a non-Hadoop cluster are welcome as well. The core libraries are highly optimized to allow for good performance also for non-distributed algorithms. Scalable to support your business case. Mahout is distributed under a commercially friendly Apache Software license. Scalable community. The goal of Mahout is to build a vibrant, responsive, diverse community to facilitate discussions not only on the project itself but also on potential use cases. Come to the mailing lists to find out more. Currently Mahout supports mainly four use cases: Recommendation mining takes users' behavior and from that tries to find items users might like. Clustering takes e.g. text documents and groups them into groups of topically related documents. Classification learns from existing categorized documents what documents of a specific category look like and is able to assign unlabelled documents to the (hopefully) correct category. Frequent itemset mining takes a set of item groups (terms in a query session, shopping cart content) and identifies, which individual items usually appear together.

# pact-jvm-consumer-java8 Provides a Java8 lambda based DSL for use with Junit to build consumer tests. # A Lambda DSL for Pact This is an extension for the pact DSL provided by [pact-jvm-consumer](../pact-jvm-consumer). The difference between the default pact DSL and this lambda DSL is, as the name suggests, the usage of lambdas. The use of lambdas makes the code much cleaner. ## Why a new DSL implementation? The lambda DSL solves the following two main issues. Both are visible in the following code sample: ```java new PactDslJsonArray() .array() # open an array .stringValue(&quot;a1&quot;) # choose the method that is valid for arrays .stringValue(&quot;a2&quot;) # choose the method that is valid for arrays .closeArray() # close the array .array() # open an array .numberValue(1) # choose the method that is valid for arrays .numberValue(2) # choose the method that is valid for arrays .closeArray() # close the array .array() # open an array .object() # now we work with an object .stringValue(&quot;foo&quot;, &quot;Foo&quot;) # choose the method that is valid for objects .closeObject() # close the object and we&apos;re back in the array .closeArray() # close the array ``` ### The existing DSL is quite error-prone Methods may only be called in certain states. For example `object()` may only be called when you&apos;re currently working on an array whereas `object(name)` is only allowed to be called when working on an object. But both of the methods are available. You&apos;ll find out at runtime if you&apos;re using the correct method. Finally, the need for opening and closing objects and arrays makes usage cumbersome. The lambda DSL has no ambiguous methods and there&apos;s no need to close objects and arrays as all the work on such an object is wrapped in a lamda call. ### The existing DSL is hard to read When formatting your source code with an IDE the code becomes hard to read as there&apos;s no indentation possible. Of course, you could do it by hand but we want auto formatting! Auto formatting works great for the new DSL! ```java array.object((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); # an attribute o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); # an attribute o.object(&quot;tar&quot;, (tarObject) -&gt; { # an attribute with a nested object tarObject.stringValue(&quot;a&quot;, &quot;A&quot;); # attribute of the nested object tarObject.stringValue(&quot;b&quot;, &quot;B&quot;); # attribute of the nested object }) }); ``` ## Installation ### Maven ``` &lt;dependency&gt; &lt;groupId&gt;au.com.dius&lt;/groupId&gt; &lt;artifactId&gt;pact-jvm-consumer-java8_2.12&lt;/artifactId&gt; &lt;version&gt;${pact.version}&lt;/version&gt; &lt;/dependency&gt; ``` ## Usage Start with a static import of `LambdaDsl`. This class contains factory methods for the lambda dsl extension. When you come accross the `body()` method of `PactDslWithProvider` builder start using the new extensions. The call to `LambdaDsl` replaces the call to instance `new PactDslJsonArray()` and `new PactDslJsonBody()` of the pact library. ```java io.pactfoundation.consumer.dsl.LambdaDsl.* ``` ### Response body as json array ```java import static io.pactfoundation.consumer.dsl.LambdaDsl.newJsonArray; ... PactDslWithProvider builder = ... builder.given(&quot;some state&quot;) .uponReceiving(&quot;a request&quot;) .path(&quot;/my-app/my-service&quot;) .method(&quot;GET&quot;) .willRespondWith() .status(200) .body(newJsonArray((a) -&gt; { a.stringValue(&quot;a1&quot;); a.stringValue(&quot;a2&quot;); }).build()); ``` ### Response body as json object ```java import static io.pactfoundation.consumer.dsl.LambdaDsl.newJsonBody; ... PactDslWithProvider builder = ... builder.given(&quot;some state&quot;) .uponReceiving(&quot;a request&quot;) .path(&quot;/my-app/my-service&quot;) .method(&quot;GET&quot;) .willRespondWith() .status(200) .body(newJsonBody((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); }).build()); ``` ### Examples #### Simple Json object When creating simple json structures the difference between the two approaches isn&apos;t big. ##### JSON ```json { &quot;bar&quot;: &quot;Bar&quot;, &quot;foo&quot;: &quot;Foo&quot; } ``` ##### Pact DSL ```java new PactDslJsonBody() .stringValue(&quot;foo&quot;, &quot;Foo&quot;) .stringValue(&quot;bar&quot;, &quot;Bar&quot;) ``` ##### Lambda DSL ```java newJsonBody((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); }).build(); ``` #### An array of arrays When we come to more complex constructs with arrays and nested objects the beauty of lambdas become visible! ##### JSON ```json [ [&quot;a1&quot;, &quot;a2&quot;], [1, 2], [{&quot;foo&quot;: &quot;Foo&quot;}] ] ``` ##### Pact DSL ```java new PactDslJsonArray() .array() .stringValue(&quot;a1&quot;) .stringValue(&quot;a2&quot;) .closeArray() .array() .numberValue(1) .numberValue(2) .closeArray() .array() .object() .stringValue(&quot;foo&quot;, &quot;Foo&quot;) .closeObject() .closeArray(); ``` ##### Lambda DSL ```java newJsonArray((rootArray) -&gt; { rootArray.array((a) -&gt; a.stringValue(&quot;a1&quot;).stringValue(&quot;a2&quot;)); rootArray.array((a) -&gt; a.numberValue(1).numberValue(2)); rootArray.array((a) -&gt; a.object((o) -&gt; o.stringValue(&quot;foo&quot;, &quot;Foo&quot;))); }).build(); ``` `object` is a reserved word in Kotlin. To allow using the DSL without escaping, a Kotlin extension `newObject` is available: ```kotlin newJsonArray { rootArray -&gt; rootArray.array { a -&gt; a.stringValue(&quot;a1&quot;).stringValue(&quot;a2&quot;) } rootArray.array { a -&gt; a.numberValue(1).numberValue(2) } rootArray.array { a -&gt; a.newObject { o -&gt; o.stringValue(&quot;foo&quot;, &quot;Foo&quot;) } } }.build(); ```

# pact-jvm-consumer-java8 Provides a Java8 lambda based DSL for use with Junit to build consumer tests. # A Lambda DSL for Pact This is an extension for the pact DSL provided by [pact-jvm-consumer](../pact-jvm-consumer). The difference between the default pact DSL and this lambda DSL is, as the name suggests, the usage of lambdas. The use of lambdas makes the code much cleaner. ## Why a new DSL implementation? The lambda DSL solves the following two main issues. Both are visible in the following code sample: ```java new PactDslJsonArray() .array() # open an array .stringValue(&quot;a1&quot;) # choose the method that is valid for arrays .stringValue(&quot;a2&quot;) # choose the method that is valid for arrays .closeArray() # close the array .array() # open an array .numberValue(1) # choose the method that is valid for arrays .numberValue(2) # choose the method that is valid for arrays .closeArray() # close the array .array() # open an array .object() # now we work with an object .stringValue(&quot;foo&quot;, &quot;Foo&quot;) # choose the method that is valid for objects .closeObject() # close the object and we&apos;re back in the array .closeArray() # close the array ``` ### The existing DSL is quite error-prone Methods may only be called in certain states. For example `object()` may only be called when you&apos;re currently working on an array whereas `object(name)` is only allowed to be called when working on an object. But both of the methods are available. You&apos;ll find out at runtime if you&apos;re using the correct method. Finally, the need for opening and closing objects and arrays makes usage cumbersome. The lambda DSL has no ambiguous methods and there&apos;s no need to close objects and arrays as all the work on such an object is wrapped in a lamda call. ### The existing DSL is hard to read When formatting your source code with an IDE the code becomes hard to read as there&apos;s no indentation possible. Of course, you could do it by hand but we want auto formatting! Auto formatting works great for the new DSL! ```java array.object((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); # an attribute o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); # an attribute o.object(&quot;tar&quot;, (tarObject) -&gt; { # an attribute with a nested object tarObject.stringValue(&quot;a&quot;, &quot;A&quot;); # attribute of the nested object tarObject.stringValue(&quot;b&quot;, &quot;B&quot;); # attribute of the nested object }) }); ``` ## Installation ### Maven ``` &lt;dependency&gt; &lt;groupId&gt;au.com.dius&lt;/groupId&gt; &lt;artifactId&gt;pact-jvm-consumer-java8_2.12&lt;/artifactId&gt; &lt;version&gt;${pact.version}&lt;/version&gt; &lt;/dependency&gt; ``` ## Usage Start with a static import of `LambdaDsl`. This class contains factory methods for the lambda dsl extension. When you come accross the `body()` method of `PactDslWithProvider` builder start using the new extensions. The call to `LambdaDsl` replaces the call to instance `new PactDslJsonArray()` and `new PactDslJsonBody()` of the pact library. ```java io.pactfoundation.consumer.dsl.LambdaDsl.* ``` ### Response body as json array ```java import static io.pactfoundation.consumer.dsl.LambdaDsl.newJsonArray; ... PactDslWithProvider builder = ... builder.given(&quot;some state&quot;) .uponReceiving(&quot;a request&quot;) .path(&quot;/my-app/my-service&quot;) .method(&quot;GET&quot;) .willRespondWith() .status(200) .body(newJsonArray((a) -&gt; { a.stringValue(&quot;a1&quot;); a.stringValue(&quot;a2&quot;); }).build()); ``` ### Response body as json object ```java import static io.pactfoundation.consumer.dsl.LambdaDsl.newJsonBody; ... PactDslWithProvider builder = ... builder.given(&quot;some state&quot;) .uponReceiving(&quot;a request&quot;) .path(&quot;/my-app/my-service&quot;) .method(&quot;GET&quot;) .willRespondWith() .status(200) .body(newJsonBody((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); }).build()); ``` ### Examples #### Simple Json object When creating simple json structures the difference between the two approaches isn&apos;t big. ##### JSON ```json { &quot;bar&quot;: &quot;Bar&quot;, &quot;foo&quot;: &quot;Foo&quot; } ``` ##### Pact DSL ```java new PactDslJsonBody() .stringValue(&quot;foo&quot;, &quot;Foo&quot;) .stringValue(&quot;bar&quot;, &quot;Bar&quot;) ``` ##### Lambda DSL ```java newJsonBody((o) -&gt; { o.stringValue(&quot;foo&quot;, &quot;Foo&quot;); o.stringValue(&quot;bar&quot;, &quot;Bar&quot;); }).build(); ``` #### An array of arrays When we come to more complex constructs with arrays and nested objects the beauty of lambdas become visible! ##### JSON ```json [ [&quot;a1&quot;, &quot;a2&quot;], [1, 2], [{&quot;foo&quot;: &quot;Foo&quot;}] ] ``` ##### Pact DSL ```java new PactDslJsonArray() .array() .stringValue(&quot;a1&quot;) .stringValue(&quot;a2&quot;) .closeArray() .array() .numberValue(1) .numberValue(2) .closeArray() .array() .object() .stringValue(&quot;foo&quot;, &quot;Foo&quot;) .closeObject() .closeArray(); ``` ##### Lambda DSL ```java newJsonArray((rootArray) -&gt; { rootArray.array((a) -&gt; a.stringValue(&quot;a1&quot;).stringValue(&quot;a2&quot;)); rootArray.array((a) -&gt; a.numberValue(1).numberValue(2)); rootArray.array((a) -&gt; a.object((o) -&gt; o.stringValue(&quot;foo&quot;, &quot;Foo&quot;))); }).build(); ``` ##### Kotlin Lambda DSL ```kotlin newJsonArray { newArray { stringValue(&quot;a1&quot;) stringValue(&quot;a2&quot;) } newArray { numberValue(1) numberValue(2) } newArray { newObject { stringValue(&quot;foo&quot;, &quot;Foo&quot;) } } } ```