Admin Console - adding metadata to openBIS from command line

What is Admin Console?

openBIS Admin Console is a command line tool which allows to add metadata to openBIS using a simple scripting language.
It is particulary useful when one has to perform property types assignments many times, Admin Console allows to do that much faster compared to the web browser interface.
It can:

• create sample/experiment/dataset/material types
• create property types and assign them to sample/experiment/dataset/material types

How to run Admin Console

• extract openbis-admin-console.jar from the from the openBIS Application Server installation package. You can find it in:

  openBIS-server-*.zip / openBIS-server / openbis-admin-console.zip / openbis-admin-console / openbis-admin-console.jar
  

• create a file with commands. See the Syntax and Example chapter to learn how to write them. Launch the Admin Console specifying the file as a parameter:

  java -jar openbis-admin-console.jar <OPENBIS-URL>/openbis/openbis commands.txt <USER> [<PASSWORD>]
  

  where:
  • <OPENBIS-URL> is openBIS server URL
  • <USER> is the openBIS user login
• if <PASSWORD> is not specified the console will ask for it

Syntax

• to define a variable X and assign it the value V :

    set X = V
  

• write ${X} to reference X variable from other places.
• comment lines should be started with --
• to register sample/experiment/dataset/material type:

  register-type <ENTITY-KIND> <ENTITY-TYPE>
  

  where:
  • <ENTITY-KIND> - one of SAMPLE, EXPERIMENT, DATA_SET or MATERIAL
  • <ENTITY-TYPE> - sample/experiment/dataset/material type code
  • when registerting a sample type one can additionally specify following sample type attributes:

    listable=<false/true> show-container=<false/true> show-parents=<false/true>
    

• to create a property with code <PROPERTY-CODE>, label <PROPERTY-LABEL> and type <DATA-TYPE> type:

  register-property-type <PROPERTY-CODE> with data type <DATA-TYPE> "label=<PROPERTY-LABEL>" "description=<PROPERTY-DESCRPTION>"
  

  Possible values of <DATA-TYPE> are:

  INTEGER, VARCHAR, MULTILINE_VARCHAR, REAL, TIMESTAMP, BOOLEAN, CONTROLLEDVOCABULARY(<VOCABULARY_CODE>),
  MATERIAL, MATERIAL(<MATERIAL_TYPE_CODE>),
  HYPERLINK, XML
  

• to assign property type to the sample/experiment/dataset/material type:

  assign-to <ENTITY-KIND>:<ENTITY-TYPE> <PROPERTY-CODE> [mandatory]
  

  where:
  • <ENTITY-KIND> - one of SAMPLE, EXPERIMENT, DATA_SET or MATERIAL
  • <ENTITY-TYPE> - sample/experiment/dataset/material type code

Examples

To execute commands from commands.txt file on the infectx.biozentrum.unibas.ch server type:

java -jar openbis-admin-console.jar https://infectx.biozentrum.unibas.ch/openbis/openbis commands.txt admin@unibas.ch

where commands.txt file contains e.q.:

-- Experiment

set type = OBSERVER_EMAILS
register-property-type ${type} with data type VARCHAR "label=Observer e-mails"
assign-to EXPERIMENT:COMPOUND_HCS ${type}

set type = LIBRARY_TEMPLATE
register-property-type ${type} with data type MULTILINE_VARCHAR "label=Library Template"
assign-to EXPERIMENT:COMPOUND_HCS ${type}


-- Sample

register-type SAMPLE POSITIVE_CONTROL listable=false show-container=true show-parents=false
register-type SAMPLE NEGATIVE_CONTROL listable=false show-container=true show-parents=false
register-type SAMPLE COMPOUND_WELL listable=false show-container=true show-parents=false

set type = CONCENTRATION_M
register-property-type ${type} with data type REAL "label=Concentration (M)"
assign-to SAMPLE:COMPOUND_WELL ${type}

set type = COMPOUND
register-property-type ${type} with data type MATERIAL(COMPOUND) "label=Compound"
assign-to SAMPLE:COMPOUND_WELL ${type}


--  Materials

set type = COMPOUND_ID
register-property-type ${type} with data type VARCHAR
assign-to MATERIAL:COMPOUND ${type}

set type = COMPOUND_BATCH_ID
register-property-type ${type} with data type VARCHAR "label=Compound Batch"
assign-to MATERIAL:COMPOUND ${type}

-- Data Sets

set type = ACQUISITION_BATCH
register-property-type ${type} with data type VARCHAR "label=Acquisition Batch"
assign-to DATA_SET:HCS_IMAGE_RAW ${type}