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

The microscopy 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 Microscopy and Flow Core Technologies are installed along with openBIS and are ready to use. Still, some configuration is possible as explained in the following.

Microscopy Core Technology configuration

The root folder of the Microscopy Core Technology is:

${MICROSCOPY_ROOT} = ${OPENBIS_ROOT}/servers/core-plugins/microscopy

Web applications

The two configuration files are:

${MICROSCOPY_ROOT}/2/as/webapps/microscopy-experiment-viewer/html/etc/config.js
${MICROSCOPY_ROOT}/2/as/webapps/microscopy-viewer/html/etc/config.js

 The two files are identical and should remain identical. The content of the files 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 to true to enable an action button "Export to your HRM source folder" to export
// the data to the source folder of the Huygens Remote Manager as configured in
// `dss/reporting-plugins/export_microscopy_datasets/plugin.properties`.
//
// Possible values: true | false.
CONFIG.enableExportToHRMSourceFolder = 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 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).

If CONFIG.enableExportToHRMSourceFolder is set to true, an action button Export to your HRM source folder will appear in the web applications to export the data to the source folder of the Huygens Remote Manager configured by the administrator (see below).

The third 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 files are left untouched on openBIS upgrades!

Core plug-ins

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

${MICROSCOPY_ROOT}/2/dss/reporting-plugins/export_microscopy_datasets/plugin.properties

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) and/or
# into the HRM source folder. Both are optional and can be disabled in the
# configuration files of the microscopy-experiment-viewer and microscopy-viewer
# web apps.
#
# 1) Generic directory
#
# 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
#
# 2) Huygens Remote Manager source directory
#
# The same considerations hold as for 1). The directory is constructed as follows:
#
#     ${hrm_base_dir}/${username}/${hrm_src_subdir}
#
# As an example, if ${hrm_base_dir} is '/data' and ${hrm_src_subdir} is 'src',
# when user 'jpe' triggers the plug-in from openBIS, the data will be copied to:
#
#
#    /data/joe/src
#
# Generic folder
base_dir =
export_dir =
 
# HRM source folder
hrm_base_dir =
hrm_src_subdir =

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

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

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