Child pages
  • Flow cytometry plug-in configuration
Skip to end of metadata
Go to start of metadata

These configuration steps are only required for the standard user interface. No additional configuration is required for the ELN-LIMS integration!

The upgrade from openBIS 16.05 to 18.06 does not migrate the configuration for the flow cytometry core technology. Please see the notes below.

The flow cytometry core technology require Jython 2.7 to run. Please see Jython Version for Various Plugins on how to set up openBIS to use Jython 2.7 (default as of version S228) instead of 2.5.

The root folder of the Flow Core Technology is:

${FLOW_ROOT} = ${OPENBIS_ROOT}/servers/core-plugins/flow

Web applications

The configuration file is:

${FLOW_ROOT}/2/as/webapps/flow-viewer/html/etc/config.js

Please notice that in version 1 of the flow cytometry core technology, the path was: ${FLOW_ROOT}/1/as/webapps/bdfacsdiva-viewer/html/etc/config.js. The upgrade to openBIS 18.06 does not migrate this file. Please do it manually!

The content of the file is:

/**
 * This file configures the web application.
 */
 
// WEB APPLICATION CONFIGURATION SETTINGS
var CONFIG = {};

// Set to true to enable an action button "Export to your user folder"
// to export the data to the user folder as configured in
// `dss/reporting-plugins/export_microscopy_datasets/plugin.properties`.
//
// Possible values: true | false.
CONFIG.enableExportToUserFolder = false;

// Set the target datastore server if the default value ("DSS1") is not correct.
//
// See variable `data-store-server-code` in DSS configuration file
// `openbis/servers/datastore_server/etc/service.properties'.
CONFIG.dataStoreServer = "DSS1";
If enableExportToUserFolder is set to true, an action button Export to your user folder will appear in the web applications to export the data to the user folder configured by the administrator (see below).

If CONFIG.enableExportToUserFolder is set to true, an action button Export to your user folder will appear in the web applications to export the data to the user folder configured by the administrator (see below).

The alternative option to export data from openBIS is via a Download action button that allows to download the data via the browser. This option is always on.

The target datastore server can be defined here if the default value (DSS1) is not correct.

Please note that the configuration file is left untouched on openBIS upgrades!

Core plug-ins

The file allows to configure the user folder used by the web application. You can find the documentation in the configuration file itself (reproduced below). The file is:

${FLOW_ROOT}/2/dss/reporting-plugins/export_flow_datasets/plugin.properties

Please notice that in version 1 of the flow cytometry core technology, the path was: ${FLOW_ROOT}/1/dss/reporting-plugins/export_bdfacsdiva_datasets/plugin/properties. The upgrade to openBIS 18.06 does not migrate this file. Please do it manually!

The configuration file is documented.

{Do not modify anything above this line!}
 
# Custom plug-in settings
#
# This plug-in exports the selected datasets to a specific directory on
# the same file system as the DSS (it can of course be a network mount).
#
#
# The actual directory is a constructed from three parts:
#
#     ${base_dir}/${username}/${export_dir}
#
# ${base_dir} is common to all users, ${username} is provided by openBIS at
# runtime and maps to the user currently logged in, and ${export_dir} is a
# specific sub-folder in ${base_dir}/${username} where the files are copied.
#
# ${export_dir} is meant to prevent that files are dumped wildly at the root
# of, e.g., the user's home folder.
#
# In a simplified, but unlikely, example case, ${base_dir} could be '/home',
# and ${export_dir} could be 'openbis_export', so that when user 'joe' triggers
# the plug-in from openBIS, his data will be copied to:
#
#    /home/joe/openbis_export
#
# Example:
#
# base_dir = /home
# export_dir = openbis_export
base_dir = 
export_dir = 

Do not touch the first four lines of the configuration file!

Please note that the configuration file is left untouched on openBIS upgrades!

  • No labels