Data Capture

The data-capture service is responsible for the capture and ingestion of data from instruments in the SynBioChem centre. It is installed inside a Java servlet container (such as Tomcat) and it assumes that it is running on a system that has both the storage system (e.g., a NAS) and the instruments mounted as remote devices. The process of doing the mounting is outside the scope of this code.

Building

This is a mavenized project; build by using mvn package. Builds produce two resulting artifacts:

1. data-capture.war — the WAR to deploy into the servlet container.
2. data-capture-dropboxes.war — the configuration of the dropboxes to deploy into OpenBIS.

Workflow

The workflow implemented on upload is described in the workflow() method of the manchester.synbiochem.datacapture.ArchiverTask class. At a high level, it does this in this order:

1. Lists the files to archive.
2. Copies the files to the working store.
3. Ingests the files into OpenBIS (via a second copy to a relevant drop-box).
4. Registers an assay in SEEK for the ingestion if an existing assay was not in use.
5. Computes the basic technical metadata for the files.
6. Bags-up the data for archive. (Not yet implemented.)
7. Stores the metadata in SEEK and on disk.