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Pinery Development Guide

Modules

Pinery is composed of several modules:

Module Contains
pinery-api data class interfaces
pinery-lims default implementations of all of the data class interfaces
pinery-service service layer interfaces and implementations; used by the webservice to retrieve data from a LIMS or cache
pinery-ws-dto data transfer objects used in responses from the webservice
pinery-ws web app using Spring Framework
pinery-client library that can be used for client applications to retrieve data from Pinery

Testing

  • Pinery-client has unit tests for all client classes
  • Pinery-service has unit tests for the provenance services
  • Pinery-ws-dto has unit tests for some of the DTO conversions
  • Pinery-ws has unit tests for the resource (Spring controller) classes
    • The versioned provenance transform tests are especially important - every provenance version being served should have a test that checks to ensure the hash never changes

Writing a New Implementation

  • Provide an implementation of the ca.on.oicr.pinery.api.Lims interface

  • Include an internal spring config XML in src/main/resources/ declaring a bean of the Lims implementation type. Any other wiring necessary for the implementation may be included. This file should be named specifically to avoid collisions. pinery-mylims-config.xml is an ideal name, whereas a name like context.xml is more likely to cause problems with other similarly named files in the classpath.

  • Include an example external context.xml that can be copied when deploying to Tomcat. This file should set the active Spring profile to external, and provide the names of the internal spring config XML described above and the properties file that will contain any other configuration. For example:

    <Context>
  <Parameter name="spring.profiles.active" value="external" override="false"/>
  <Parameter name="pinery.external.springConfigFile" value="mylims-config.xml"/>
  <Parameter name="pinery.propertiesFile" value="file:${CATALINA_HOME}/conf/Catalina/localhost/pinery-mylims.properties" override="false"/>
</Context>

  • Include an example properties file containing any options that are necessary (DB connection info, API keys, etc.)

  • Package the external module as a war and include pinery-ws as an overlay. Example Maven config:

    <packaging>war</packaging>

<dependencies>
  <dependency>
    <groupId>ca.on.oicr</groupId>
    <artifactId>pinery-ws</artifactId>
    <version>${pinery.version}</version>
    <type>war</type>
    <scope>runtime</scope>
  </dependency>
  ...
</dependencies>