screeningBee Data Analysis Tools

OpenBIS Properties in Bee and on the Cluster

When the Bee stages datasets on the processing scratch space (cluster) it creates for each dataset a metadata properties file containing some dataset information coming from OpenBIS.

The file is to be found in the dataset cache directory and its name is bee_storage_provider.properties. E.g.:

...../BeeDatasetCache/20121012004835955-27454/bee_storage_provider.properties

Which dataset information

1. OpenBIS dataset code

In property with name DATASET_ID.

2. OpenBIS dataset type

In property with name DATASET_TYPE.

3. OpenBIS dataset experiment name

In property with name EXPERIMENT_NAME.

4. OpenBIS dataset sample name

In property with name SAMPLE_NAME.
The sample name will be extracted from the dataset itself, or from its container if the dataset is a contained one.

5. OpenBIS dataset properties

Both, the names and values of the properties are provided by OpenBIS.
If the dataset is a contained dataset, the metadata file will contain the properties from the dataset itself and the properties from its container.
If the dataset is not a contained dataset, the metadata file will contain the properties from the dataset itself.

Examples of 'bee_storage_provider.properties' files

Examples are taken from the OpenBIS instance installed in STAGE.

Dataset 20130215175757007-40162

#Tue Sep 10 16:17:59 GMT+01:00 2013
DATASET_ID=20130215175757007-40162
SAMPLE_NAME=/INFECTX/DZ07-1K
IBRAIN2.DATASET.ID=2348
INSTRUMENT.ID=BS-IX1
DATASET_TYPE=HCS_IMAGE_RAW
FILESIZE_SUM=24181862
IMAGE_COUNT=13824
EXPERIMENT_NAME=/INFECTX/LISTERIA_TEAM/LISTERIA-DP-G1
ACQUISITION.TIMESTAMP=03FC58BC
CHANNEL_LIST=Cy3,Cy5,DAPI,GFP

Dataset 20121123170634713-34193

#Wed Apr 10 16:30:23 GMT+02:00 2013
DATASET_ID=20121123170634713-34193
IBRAIN2.DATASET.ID=2131
IBRAIN2.MODULE.ORDER=1
SAMPLE_NAME=/BEE/KB2-09-1E
DATASET_TYPE=CLUSTER_JOB_LOGS
IBRAIN2.WORKFLOW.ID=61
IBRAIN2.PARENT.DATASET.ID=1955
IBRAIN2.WORKFLOW.NAME=VacciniaShdCrrVer010MD3R2011b
IBRAIN2.PROCESS.ID=339
$ANALYSIS_PROCEDURE=VacciniaShdCrrVer010MD3R2011b (emmenlau)
EXPERIMENT_NAME=/BEE/VACCINIA_TEAM/VACCINIA-AU-K1
IBRAIN2.WORKFLOW.AUTHOR=emmenlau