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Core Plugins

Motivation

The service.properties file of openBIS Application Server (AS) and Data Store Server (DSS) can be quite big because of all the configuration data for maintenance tasks, drop-boxes, reporting and processing plugins, etc. Making this configuration more modular will improve the structure. It would also allow to have core plugins shipped with distribution and customized plugins separately. This make maintenance of these plugins more independent. For example, a new maintenance task plugin can be added in an update without any need for an admin to put the configuration data manually into the service.properties file.

Core Plugins Folder Structure

All plugins whether they are a part of the distribution or added and maintained are store in a folder usually called core-plugins. Standard (i.e. core) plugins are part of distribution. During installation the folder core-plugins is unpacked as a sibling folder of openBIS-server and datastore_server.

The folder structure is organized as follows:

  • The file core-plugins.properties containing the following properties:
    • enabled-modules: comma-separated list of regular expressions for all enabled modules.
    • disabled-core-plugins: comma-separated list of disabled plugins. All plugins are disabled for which the beginning of full plugin ID matches one of the terms of this list. To disable initialization of master data of a module - disable it's core plugin "initialize-master-data"
  • The children of core-plugins are folders denoting modules like the standard technologies proteomics and screening. For customization any module can be added.
  • Each module folder has children which are numbered folders. The number denote the version of the plugins of that module. The version with largest number will be used. Different modules can have different largest version numbers.
  • A version folder has the subfolder as and/or dss which has subfolders for the various types of plugins. The types are different for AS and DSS:
    • AS:
      • maintenance-tasks: Maintenance tasks triggered by some time schedule.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.common.maintenance.IMaintenanceTask.
        For more details see Maintenance Tasks.
      • dss-data-sources: Definition of data sources with corresponding data source definitions for DSS. For more details see Installation and Administrator Guide of the openBIS Server.
      • query-databases: Databases for SQL queries. For more details see Custom Database Queries.
      • custom-imports: Custom file imports to DSS via Web interface. For more details see Custom Import.
      • services: Custom services. For more details see Custom Application Server Services.
      • webapps: HTML5 applications that use the openBIS API. For more details see openBIS webapps.
      • miscellaneous: Any additional properties.
    • DSS:
      • drop-boxes: ETL server threads for registration of data sets.
      • reporting-plugins: Reports visible in openBIS.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask.
        For more details see Reporting Plugins.
      • processing-plugins: Processing tasks triggered by users.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask.
        For more details see Processing Plugins.
      • maintenance-tasks: Maintenance tasks triggered by some time schedule.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.common.maintenance.IMaintenanceTask.
        For more details see Maintenance Tasks.
      • search-domain-services: Services for variaous search domains (e.g. search on sequence databases using BLAST).
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService.
      • data-sources: Internal or external database sources.
      • services: Services based on servlets.
        Property class denotes fully-qualified class name of a class implementing javax.servlet.Servlet.
      • imaging-overview-plugins: Data set type specific provider of the overview image of a data set.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.openbis.dss.generic.server.IDatasetImageOverviewPlugin.
      • file-system-plugins: Provider of a custom DSS file system (FTP/SFTP) view hierarchy.
        Property class denotes fully-qualified class name of a class implementing ch.systemsx.cisd.openbis.dss.generic.server.fs.IResolverPlugin
        Property code denotes the name of the top-level directory under which the custom hierarchy will be visible
      • miscellaneous: Any additional properties.
  • Each of these types folder can have an arbitrary number of subfolders. But if the type folder is present it should have at least one subfolder. Each defining one plugin. The name of these subfolders defining the plugin ID. It has to be unique over all plugins independent of module and plugin type. It should not contain the characters  space ' ', comma ',', and equal sign '='.
  • Each plugin folder should contain at least the file plugin.properties. There could be additional files (referred in plugin.properties) but no subfolders.

Here is an example of a typical structure of a core plugins folder:

core-plugins
  core-plugins.properties
  proteomics
    1
      as
        initialize-master-data.py
      dss
        drop-boxes
          ms-injection
            plugin.properties
        maintenance-tasks
          data-set-clean-up
            plugin.properties
  screening
    1
      core-plugin.properties
      as
        initialize-master-data.py
        maintenance-tasks
          material-reporting
            mapping.txt
            plugin.properties
        custom-imports
          myCustomImport
            plugin.properties
      dss
        drop-boxes
          hcs-dropbox
            lib
              custom-lib.jar
            hcs-dropbox.py
            plugin.properties

You might noticed the file initialize-master-data.py in AS core plugins sections  in this example. It is a script to register master data in the openBIS core database. For more details see Installation and Administrator Guide of the openBIS Server.

Each plugin can refer to any number of files. These files are part of the plugin folder. In plugin.properties they are referred relative to the plugin folder, that is by file name. Example:

plugin.properties
incoming-dir = ${incoming-root-dir}/incoming-hcs
incoming-data-completeness-condition = auto-detection
top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
script-path = hcs-dropbox.py
storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
storage-processor.data-source = imaging-db
storage-processor.define-channels-per-experiment = false

Merging Configuration Data

At start up of AS and DSS merges  the content of  service.properties with the content of all plugin.properties of the latest version per enabled module. Plugin properties can be deleted by adding <plugin ID>.<plugin property key> = __DELETED__ to service.properties. Example:

simple-dropbox.incoming-data-completeness-condition = __DELETED__

This leads to a deletion of the property incoming-data-completeness-condition specified in plugins.properties of the plugin simple-dropbox.

Merging is done by injection the properties of plugin.properties into service.properties by adding the plugin ID as a prefix to the property key (not for miscellaneous). For example, the property script-path of plugin hcs-dropbox becomes hcs-dropbox.script-path. References to files inside the plugin are replaced by a path relative to the working directory. For the various plugin types (except miscellaneous) the plugin ID is append to the related property in  service.properties for this plugin type. For example, plugins of type drop-boxes are added to the property inputs.

Enabling Modules and Disabling Plugins

There are three methods to control which plugins are available and witch not:

  • enabling by property enabled-modules in core-plugins.properties: This enables all plugins of certain modules.
  • disabling by property disabled-core-plugins in core-plugins.properties : This allows to disable on a fine grade level specific plugins.
  • disabling by marker file: Plugin developers should use this method when developing new plugins.

Enabling Modules

The property enabled-modules in core-plugins.properties is a comma-separated list of regular expressions denoting modules. All plugins in a module folder of core-plugins folder are enabled if the module name matches one of these regular expressions. If this list is empty or the property hasn't been specified no core-plugin will be used. Note, that this property is manipulated by openBIS Installer for Standard Technologies. Example:

service.properties
enabled-modules = screening, proteomics, dev-module-.*

Disabling Core Plugins by Property

The property disabled-core-plugins in core-plugins.properties allows to disable plugins selectively either by module name, module combined with plugin type or full plugin ID. Example:

service.properties
disabled-core-plugins = screening, proteomics:reporting-plugins, proteomics:maintenance-tasks:data-set-clean-up

Disabling Core Plugins by Marker File

The empty marker file disabled in a certain plugin folder disables the particular plugin.

Core Plugin Dependency

A core plugin can depend on another core plugin. The dependency is specified in <module>/<version>/core-plugin.properties. It has a property named required-plugins. Its value is a comma-separated list of core-plugins on which it depend. The dependency can be specified selectively either by module name, module combined with plugin type or full plugin ID. Example:

core-plugin.properties
required-plugins = module-a, module-b:initialize-master-data, module-b:reporting-plugins, module-a:drop-boxes:generic

Rules for Plugin Writers

As a consequence of the way plugins are merged with  service.properties writers of plugins have to obey the following rules:

  • Plugin IDs have to be unique among all plugins whether they are defined in service.properties or as core plugins. The only exceptions are plugins of type miscellaneous.
  • In plugin.properties other properties can be referred by the usual ${<property key>} notation. The referred property can be in service.properties or in any plugin.properties.
  • As convention use ${incoming-root-dir} when defining the incoming folder for a drop box.
  • Refer files in plugin.properties only by names and add them as siblings of plugin.properties to the plugin folder. Note, that different plugins can refer files with the same name. There will be no ambiguity which file is meant.
  • In order to be completely independent from updates of the core plugins which are part of the distribution create your own module, like my-plugins, and put all your plugins there. Do not forget to add your module to the property enabled-modules in core-plugins.properties.

Using Java libraries in Core Plugins

OpenBIS allows you to include Java libraries in core plugin folders. The *.jar files have to be stored in "<code plugin folder>/lib" folder. For instance, in order to use "my-lib.jar" in "my-dropbox" a following file structure is needed:

service.properties
my-technology
    1
      dss
        drop-boxes
          my-dropbox
            lib
              my-lib.jar
            dropbox.py
            plugin.properties

Having this structure, Java classes from "my-lib.jar" can be imported and used in "dropbox.py" script.

NOTICE: Currently this feature is only supported for DSS core plugins. Under the hood, a symbolic link to a jar file is created in "datastore_server/lib" folder during DSS startup.

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