PC2Client

Introduction

We develop a convenient (fluent query API, reasonable defaults) Java client for the PC2 web services to use in other projects, such as in desktop Cytoscape apps, to quickly start exploring and querying the integrated PC BioPAX L3 database. Besides, we are not forcing anyone to use this client only; feel free to develop a simpler or more specific one.

Use

//using the Pathway Commons cPath2 web service URL (default):
CPathClient client = CPathClient.newInstance();
// then, result=client.create*Query()...result() or ...stringResult(format), etc.

in a Maven project, add to the pom.xml the following:

            <repositories>
	        <repository>
		    <id>ossrh</id>
		    <name>OSSRH Repository</name>
		    <url>https://oss.sonatype.org/content/groups/public/</url>
	        </repository>
            </repositories>
            <dependencies>
                <dependency>
                        <groupId>pathwaycommons.cpath</groupId>
                        <artifactId>cpath-client</artifactId>
                        <version>10.0.0-SNAPSHOT</version>
                </dependency>
                <dependency>
                        <groupId>org.biopax.paxtools</groupId>
                        <artifactId>paxtools-core</artifactId>
                        <version>5.1.0-SNAPSHOT</version>
                </dependency>
            </dependencies>

See also:

• the project's tests can be used as example;

Alternatively, one can add the cpath-client fat jar with dependencies to a Java (or JPype) project: grab the latest fat-jar (from here).

Other/Links

• http://www.biopax.org
• http://www.biopax.org/paxtools