Introduction
openBIS defines as "Master data" all metadata configurations needed before the import of the real raw data. Master data includes experiment/sample/data set/property/file types, vocabularies and property assignments.
API Basics
Similarly to the Jython Dropbox API the script can access a global variable named service, which can be used to create transactions.
transaction = service.transaction()
The transactions are a focal API concept offering to create new types (e.g. createNewSampleType, createNewDataSetType) and new property assignments (e.g. assignPropertyType).
The complete Javadoc for the API is available at
The global service variable | |
The public API of the transaction objects | |
Javadocs for the complete API package |
Simple example
import ch.systemsx.cisd.openbis.generic.client.jython.api.v1.DataType as DataType
tr = service.transaction()
expType = tr.createNewExperimentType('EXPERIMENT-TYPE')
expType.setDescription('Experiment type description.')
sampleType = tr.createNewSampleType('SAMPLE-TYPE')
sampleType.setDescription('Sample type description.')
sampleType.setSubcodeUnique(True)
sampleType.setAutoGeneratedCode(True)
sampleType.setGeneratedCodePrefix("G_");
dataSetType = tr.createNewDataSetType('DATA-SET-TYPE')
dataSetType.setContainerType(True)
dataSetType.setDescription('Data set type description.')
materialType = tr.createNewMaterialType('MATERIAL-TYPE')
materialType.setDescription('Material type description.')
stringPropertyType = tr.createNewPropertyType('VARCHAR-PROPERTY-TYPE', DataType.VARCHAR)
stringPropertyType.setDescription('Varchar property type description.')
stringPropertyType.setLabel('STRING')
materialPropertyType = tr.createNewPropertyType('MATERIAL-PROPERTY-TYPE', DataType.MATERIAL)
materialPropertyType.setDescription('Material property type description.')
materialPropertyType.setLabel('MATERIAL')
materialPropertyType.setMaterialType(materialType)
materialPropertyType.setManagedInternally(False)
# assigns the newly created property 'MATERIAL-PROPERTY-TYPE'
# as a mandatory property for 'SAMPLE-TYPE'
materialAssignment = tr.assignPropertyType(sampleType, materialPropertyType)
materialAssignment.setMandatory(True)
# assigns the newly created property 'VARCHAR-PROPERTY-TYPE'
# as an optional property for 'EXPERIMENT-TYPE' with default value 'FOO_BAR'
stringAssignement = tr.assignPropertyType(expType, stringPropertyType)
stringAssignement.setMandatory(False)
stringAssignement.setDefaultValue('FOO_BAR')
Command line tools
Executing master data scripts
Make sure openBIS AS is up and running prior script execution. Go to the openBIS AS installation folder. Assuming your script is /local/master-data-script.py and openBIS AS is started on the URL
http://localhost:8888/openbis
execute the command
> cd /local0/openbis/servers/openBIS-server/jetty/bin > /register-master-data.sh -s http://localhost:8888/openbis/openbis -f /local/master-data-script.py
You will be prompted for username/password before the script execution. Please note that the second 'openbis' is needed in the server address, so that you connect via the API.
Exporting master data
You can export the master data from a running openBIS system as script by running the command
> cd /local0/openbis/servers/openBIS-server/jetty/bin > /export-master-data.sh -s http://localhost:8888/openbis/openbis
This command will create a folder exported-master-data-DATE which will contain the exported master data script - master-data.py