Customer Use Cases

This section describes use cases for facility customers.

iRODS Data Access

In this use case, a customer downloads data that has been delivered to them by the facility staff (cf. Facility Staff Use Cases) via the iRODS iCommands.

Prerequisites

  • The user must have the iRODS iCommands command line tools installed. These are only available for Linux and MacOS. Windows users should use the WebDAV protocol.

  • The user has knowledge of the Linux/MacOS command line. Inexperienced users are recommended to use the WebDAV protocol with a graphical client.

  • The user must be able to connect to the iRODS server. For the server operated by CUBI, the client must be in the Charite/MDC/BIH networks or have appropriate VPN access.

Steps

  • Perform the iRODS setup, in particular creating a proper ~/.irods/irods_environment.json file.

  • Successfully authenticate to the iRODS server with iinit.

  • Use irsync -rkv i:${SOURCE} ${DEST} to download the data from the ${SOURCE} collection in iRODS as obtained from the data generation facility to the local destination ${DEST}.

Graphical WebDAV Data Access

In this use case, a customer downloads data that has been delivered to them by the facility staff (cf. Facility Staff Use Cases) via the WebDAV protocol using a graphical client.

Prerequisites

  • The user must have a graphical client installed that can use the WebDAV protocol. Recommended free software is:

    • WinSCP for Windows

    • Cyberduck for Mac Os X

    • The usual file browsers for Linux.

  • The user must be able to connect to the iRODS server. For the server operated by CUBI, the client must be in the Charite/MDC/BIH networks or have appropriate VPN access.

Steps

  • Connect to the RODEOS WebDAV server and login to the system.

  • Go to the location ${SOURCE} where the data for the user resides.

  • Download the data through the graphical client’s functionality (probably drag and drop).

LFTP WebDAV Data Access

In this use case, a customer downloads data that has been delivered to them by the facility staff (cf. Facility Staff Use Cases) via the WebDAV protocol using the command line client lftp.

Prerequisites

  • The user has knowledge of the Linux/Mac command line. Inexperienced users are recommended to use the WebDAV protocol with a graphical client.

  • The user must have lftp installed. The software is only available on Linux/MacOS so such an operating system is a prerequisite for installing lftp itself. Please install lftp with your Linux package manager or a tool like Homebrew for MacOS for installing lftp. If this poses a problem we recommend using one of the graphical WebDAV clients as described above.

  • The user must be able to connect to the iRODS server. For the server operated by CUBI, the client must be in the Charite/MDC/BIH networks or have appropriate VPN access.

Steps

  • Connect to the WebDAV server using the user’s account.

  • Download the data from the ${SOURCE} collection where the data for the user resides using mirror ${SOURCE} ${DEST} to the local destination directory ${DEST}.