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GlassFish build depends on properly functioning several custom lifecycle mappings and artifact handlers. Because these are necessary to resolve dependencies and to run "gf:run" goal and etc., it is critical that these extensions be made available to Maven early on during Maven execution. This definition was originally in maven-glassfish-plugin, which was integrated into Maven POM through <plugin>/<extensions>true marking, but after a series of debugging to resolve artifact resolution failure problems, it turns out that that doesn't cause Maven to load components early enough. I tried to circumbent the prolem by also registering the maven-glassfish-plugin as an extension module (via <build>/<extensions/<extension>), but that apparently confuses Maven to no end --- I get build errors like this: [INFO] Internal error in the plugin manager executing goal 'org.apache.maven.plugins:maven-jar-plugin:2.1:jar': Unable to find the mojo 'org.apache.maven.plugins:maven-jar-plugin:2.1:jar' in the plugin 'org.apache.maven.plugins:maven-jar-plugin' This is obviously one of the problematic areas of Maven, so to avoid doing hack over hack, I'm simply moving the component definitions to its own module.

Spring LDAP is a Java library for simplifying LDAP operations, based on the pattern of Spring's JdbcTemplate. The framework relieves the user of common chores, such as looking up and closing contexts, looping through results, encoding/decoding values and filters, and more. The LdapTemplate class encapsulates all the plumbing work involved in traditional LDAP programming, such as creating a DirContext, looping through NamingEnumerations, handling exceptions and cleaning up resources. This leaves the programmer to handle the important stuff - where to find data (DNs and Filters) and what do do with it (map to and from domain objects, bind, modify, unbind, etc.), in the same way that JdbcTemplate relieves the programmer of all but the actual SQL and how the data maps to the domain model. In addition to this, Spring LDAP provides transaction support, a pooling library, exception translation from NamingExceptions to a mirrored unchecked Exception hierarchy, as well as several utilities for working with filters, LDAP paths and Attributes.

GlassFish build depends on properly functioning several custom lifecycle mappings and artifact handlers. Because these are necessary to resolve dependencies and to run "gf:run" goal and etc., it is critical that these extensions be made available to Maven early on during Maven execution. This definition was originally in maven-glassfish-plugin, which was integrated into Maven POM through <plugin>/<extensions>true marking, but after a series of debugging to resolve artifact resolution failure problems, it turns out that that doesn't cause Maven to load components early enough. I tried to circumbent the prolem by also registering the maven-glassfish-plugin as an extension module (via <build>/<extensions/<extension>), but that apparently confuses Maven to no end --- I get build errors like this: [INFO] Internal error in the plugin manager executing goal 'org.apache.maven.plugins:maven-jar-plugin:2.1:jar': Unable to find the mojo 'org.apache.maven.plugins:maven-jar-plugin:2.1:jar' in the plugin 'org.apache.maven.plugins:maven-jar-plugin' This is obviously one of the problematic areas of Maven, so to avoid doing hack over hack, I'm simply moving the component definitions to its own module.

Java Prolog Interface (JPI) is an Application Provider Interface (API) for interaction between Java and Prolog programming languages. Is a bidirectional interface that communicate Java applications with Prolog program or database and Prolog procedures with Java class and methods. JPI is an abstraction layer over concrete prolog drivers over Prolog Engines. This API define all mechanism to interact with any Prolog Engine and maintain the application independent to a specific underlying engine. JPI have several connectors to open source prolog engines like SWI, YAP, XSB native engines and tuProlog, jTrolog, jLog Java based prolog engines. JPI study all related Java-Prolog integration libraries and take the betters features from each solution with the propose to achieve a common integration interface. The last feature allows switch the under laying Prolog Engine driver and the application code still be the same. JPI run over any Java Virtual Machine that support Java SE 5 or above. The project was tested over HotSpot, Open J9 and JRockit Virtual Machines over Operating Systems like Windows (7,8,10), Linux (Debian, Ubuntu) and Mac OS X. Can be deployed on Servlets Containers like Jetty, Tomcat or Glassfish Application Server. JPI can be include in any Java Project using the commonest Java Integration Development Enviroment (IDE) like Eclipse, Netbeans, IntelijIDEA and so on. JPI is developed and maintained by Prolobjectlink Project an open source initiative for build logic based applications using Prolog like fundamental Logic Programming Language in the persistence layer and application programming.

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.

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.

This project aims to offer an easy-to-extend Java DAS server framework. It offers several advantages: * Implementing data sources is very easy but also flexible and powerful. * Data caching is built into the system, with access to the caching mechanism made available to the data sources. * All aspects of the server are highly configurable, including selecting options where the DAS 1.53 specification offers choices to the implementor. * The latest Java technologies have been used throughout the system to optimise performance and simplify data source development. * Wherever possible the same terminology is used in the API as in the DAS specification and XML - again, making data source development more easy. * The server allows XSLT transforms of the DAS XML to be configured to provide a simple DAS client view (limited to the single DAS source). More details of the DAS protocol, DAS servers and DAS clients can be found at http://www.biodas.org/wiki/Main_Page. The first version of this server is a complete implementation of Distributed Sequence Annotation System (DAS) Version 1.53. If you are interested in learning more about DAS 1.53, the specification is highly recommended as a concise and complete description of the DAS protocol that can be obtained from: http://biodas.org/documents/spec.html

Chips-n-Salsa is a Java library of customizable, hybridizable, iterative, parallel, stochastic, and self-adaptive local search algorithms. The library includes implementations of several stochastic local search algorithms, including simulated annealing, hill climbers, as well as constructive search algorithms such as stochastic sampling. Chips-n-Salsa now also includes genetic algorithms as well as evolutionary algorithms more generally. The library very extensively supports simulated annealing. It includes several classes for representing solutions to a variety of optimization problems. For example, the library includes a BitVector class that implements vectors of bits, as well as classes for representing solutions to problems where we are searching for an optimal vector of integers or reals. For each of the built-in representations, the library provides the most common mutation operators for generating random neighbors of candidate solutions, as well as common crossover operators for use with evolutionary algorithms. Additionally, the library provides extensive support for permutation optimization problems, including implementations of many different mutation operators for permutations, and utilizing the efficiently implemented Permutation class of the JavaPermutationTools (JPT) library. Chips-n-Salsa is customizable, making extensive use of Java's generic types, enabling using the library to optimize other types of representations beyond what is provided in the library. It is hybridizable, providing support for integrating multiple forms of local search (e.g., using a hill climber on a solution generated by simulated annealing), creating hybrid mutation operators (e.g., local search using multiple mutation operators), as well as support for running more than one type of search for the same problem concurrently using multiple threads as a form of algorithm portfolio. Chips-n-Salsa is iterative, with support for multistart metaheuristics, including implementations of several restart schedules for varying the run lengths across the restarts. It also supports parallel execution of multiple instances of the same, or different, stochastic local search algorithms for an instance of a problem to accelerate the search process. The library supports self-adaptive search in a variety of ways, such as including implementations of adaptive annealing schedules for simulated annealing, such as the Modified Lam schedule, implementations of the simpler annealing schedules but which self-tune the initial temperature and other parameters, and restart schedules that adapt to run length.

Jsgen is a Java Source Generation Framework: That means, it should be a valuable tool, if you intend to write a custom generator for Java sources. As such, it is the successor of a previous framework, called JaxMeJS (http://jaxme.sourceforge.net/JaxMeJS/docs/index.html). The predecessor came into being as a standalone project. It was incorporated into the bigger JaxMe project, when the latter was adopted by the Apache Webservices project. And it was buried as part of the bigger project, when the latter was moved to the Apache Attic (http://svn.apache.org/repos/asf/webservices/archive/jaxme/). That was fine for quite some time, because the latest released version (JaxMeJS 0.5.2) did its job quite well. Over the years, however, the Java language has evolved, and the lack of support for features like Generics, or Annotations, became a burden. Hence the Successor: Jsgen picks up, where JaxMeJS ended. It is, however, a complete rewrite with several additional features, that the author considers to be important for modern Java applications: 1. It supports Generics. 2. It supports Annotations. 3. The builder pattern has been adopted. Almost all important classes are implemented as builders. This should make writing the actual source generators much more concise, and maintainable, than it used to be before. 4. The code style is configurable. Code styles allow you to concentrate on the actual work. The resulting Jave source will look nicely formatted, anyways. As of this writing, you can select between two builtin code styles: - The default code style is basically the authors personal free style, roughly comparable to the default code style of the Eclipse Java IDE. - As an alternative, there is also a Maven code style, which is widely used in the Open Source communities. Compared to the default style, it is less concise, if not even a bit verbose. On the other hand, it is widely adopted by projects in the vicinity of {{{https://maven.apache.org}Apache Maven}}. 5. Import lists are created, and sorted, automatically.